Article
Biology
Christopher H. Bohrer, Daniel R. Larson
Summary: The spatial organization of chromosomes plays a crucial role in gene regulation. By analyzing two recent single-cell imaging methods, we systematically investigate the impact of chromosome conformation on transcriptional regulation. Our findings suggest that physical distance, rather than genomic distance, between genes on individual chromosomes is the major factor driving co-bursting. The correlation between gene transcription decreases asymptotically to 0.3 for genes separated by less than 400 nm, highlighting the physical property of human chromosomes.
Article
Mathematics, Applied
D. N. Gerasimov
Summary: The study introduces a fractional diffusion equation for describing anomalous transport at short spatial scales, considering the anomalous diffusion phenomenon caused by non-Markovian process of scattering. The Nernst-Einstein correlation reveals the patterns of anomalous diffusion at short scales, offering an explanation for the observed dependence of conductivity in thin films on their thickness.
PHYSICA D-NONLINEAR PHENOMENA
(2021)
Article
Developmental Biology
Ha T. H. Vu, Regan L. Scott, Khursheed Iqbal, Michael J. Soares, Geetu Tuteja
Summary: In this study, the chromatin accessibility and gene regulation patterns of invasive trophoblast cells in rat and human were compared using single-nucleus ATAC-seq and single-cell RNA-seq data. Similarities in gene regulation and enriched motifs were found between the two species, and a conserved gene regulatory network in invasive trophoblast cells was identified.
Article
Biotechnology & Applied Microbiology
Dongyuan Song, Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li
Summary: We introduce a statistical simulator, scDesign3, that can generate realistic single-cell and spatial omics data by learning interpretable parameters from real data. It uses a unified probabilistic model to infer biologically meaningful parameters, assess the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations, and generate in silico negative and positive controls for benchmarking computational tools. The challenge of simulating multiomic single-cell data is addressed by a probabilistic model.
NATURE BIOTECHNOLOGY
(2023)
Article
Engineering, Electrical & Electronic
A. Herrmann, S. J. F. Erich, L. G. J. van der Ven, H. P. Huinink, W. D. van Driel, M. van Soestbergen, A. Mavinkurve, F. De Buyl, H. R. Fischer, J. M. C. Mol, O. C. G. Adan
Summary: This article investigates the influence of fillers on moisture diffusion in epoxy mold compounds and concludes that an interphase layer is present based on experimental measurements and numerical simulations.
MICROELECTRONICS RELIABILITY
(2022)
Article
Multidisciplinary Sciences
Timothy P. O'Leary, Rennie M. Kendrick, Brianna N. Bristow, Kaitlin E. Sullivan, Lihua Wang, Jody Clements, Andrew L. Lemire, Mark S. Cembrowski
Summary: This study systematically investigates the cell types of the central amygdala using single-cell RNA sequencing, fluorescent in situ hybridization, and other techniques. The researchers identify two major cell types that have not been resolved in previous studies and map their spatial distribution. The results reveal new organizational principles of cell types and spatial scales in the central amygdala, providing a framework for future research on cell-type-specific behavior and function.
Article
Multidisciplinary Sciences
Zhongli Xu, Xinjun Wang, Li Fan, Fujing Wang, Becky Lin, Jiebiao Wang, Giraldina Trevejo-Nunez, Wei Chen, Kong Chen
Summary: By analyzing lung cells from mice using multiple omics approaches, we discovered spatial and cell-type-dependent mechanisms of lung immunity.
Article
Multidisciplinary Sciences
Jiamin Yuan, Zhiqiang Liu, Yimo Wu, Jingfeng Han, Xiaomin Tang, Chengbin Li, Wei Chen, Xianfeng Yi, Jian Zhou, Rajamani Krishna, German Sastre, Anmin Zheng
Summary: Contrary to the general trend, the movement of long-chain molecules slows at higher temperatures under confinement due to the thermal resistance effect. This phenomenon limits molecular transportation in nanoscale channels, as confirmed by zero length column experiments. This study contributes to our understanding of anomalous diffusion and its mechanisms in confined systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Kateryna Fal, Niklas Korsbo, Juan Alonso-Serra, Jose Teles, Mengying Liu, Yassin Refahi, Marie-Edith Chaboute, Henrik Jonsson, Olivier Hamant
Summary: The study reveals that organogenesis in plants generates compression that has global effects on chromatin in individual cells, providing further evidence of the role of forces on chromatin changes. The research also shows that the presence of active nuclear compression in the domain where organ outgrowth occurs, suggesting a link between mechanical stress and chromatin alterations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Gastroenterology & Hepatology
Angela L. Chu, Joel D. Schilling, Kevin R. King, Ariel E. Feldstein
Summary: Single cell transcriptomics is a powerful tool for studying molecular diversity in tissues such as the liver during health and disease. By developing cell isolation and sorting protocols, researchers can more accurately analyze cell-type-specific expression and uncover the mysteries of cellular heterogeneity. Profiling transcriptomes at the single-cell level has opened up new research opportunities that were previously impossible.
Article
Biochemistry & Molecular Biology
Quan Zhang, Xiaoting Hua, Yueting Sun, Zhongying Lin, Yang Cao, Ping Zhao, Qingyou Xia
Summary: The spatial expression patterns of silk gland genes in Bombyx mori have a significant impact on their functions and silk quality. By investigating the spatial-specific expressed genes and the regulation mechanisms in the middle silk gland and posterior silk gland of silkworm, researchers identified changes in chromatin conformation and discovered the regulatory network mediated by the transcription factor POU-M2. These findings have important implications for improving silk performance, optimizing silkworm breeding, and studying the spatial regulatory models of insect genes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Anat Vivante, Irit Shoval, Yuval Garini
Summary: Lamin A plays a crucial role in maintaining nuclear organization and integrity, with its dynamics and distribution changing throughout the cell cycle. Analysis of lamin A concentration and distribution reveals its dynamic changes in different phases of the cell cycle, shedding light on its functions in nuclear assembly and disassembly.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Physics, Multidisciplinary
Philipp G. Meyer, Erez Aghion, Holger Kantz
Summary: This study is part of the 'anomalous diffusion challenge', where research teams from around the world collaborate to develop and compare new techniques for inferring stochastic models from unknown time series and estimate the anomalous diffusion exponent in data. Using numerical methods and feature analysis, this study presents an automated algorithm for model selection.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Anatomy & Morphology
Taylor Spadory, Alvaro Duque, Lynn D. Selemon
Summary: Maternal injection of H-3-thymidine during gestation has been used to study neurogenesis in different brain areas. In this study, we focused on the rostral thalamus and found that neurogenesis in the mediodorsal and anterior nuclei occurs earlier than in the lateral geniculate and pulvinar nuclei. This new understanding can contribute to our knowledge of developmental perturbation and its link to later-life incidence of schizophrenia.
BRAIN STRUCTURE & FUNCTION
(2022)
Editorial Material
Biochemistry & Molecular Biology
Zhiming Li, Zhiguo Zhang
Summary: Histone chaperones play important roles in the biogenesis, transportation, and deposition of histones, affecting processes such as DNA replication, transcription, and epigenetic inheritance. In this study, Carraro et al. uncover an interconnected chaperone network and discover a surprising function of the histone chaperone DAXX in de novo deposition of H3.3K9me3.
Article
Biophysics
Noa Plavner Hazan, Toma E. Tomov, Roman Tsukanov, Miran Liber, Yaron Berger, Rula Masoud, Katalin Toth, Joerg Langowski, Eyal Nir
BIOPHYSICAL JOURNAL
(2015)
Article
Physics, Condensed Matter
Tabea Elbel, Joerg Langowski
JOURNAL OF PHYSICS-CONDENSED MATTER
(2015)
Article
Biochemical Research Methods
Jan W. Krieger, Anand P. Singh, Nirmalya Bag, Christoph S. Garbe, Timothy E. Saunders, Joerg Langowski, Thorsten Wohland
Article
Biochemistry & Molecular Biology
Alexander Gansen, Katalin Toth, Nathalie Schwarz, Joerg Langowski
NUCLEIC ACIDS RESEARCH
(2015)
Meeting Abstract
Biophysics
Kathrin Tegeler, Johanna Mehl, Martin Wuertz, Alexander Gansen, Katalin Toth, Yaakov Levy, Joerg Langowski
BIOPHYSICAL JOURNAL
(2016)
Meeting Abstract
Biophysics
Giulia Marcarini, Jan W. Krieger, Giuseppe Chirico, Joerg Langowski
BIOPHYSICAL JOURNAL
(2016)
Article
Multidisciplinary Sciences
Gyorgy Vamosi, Norbert Muecke, Gabriele Mueller, Jan Wolfgang Krieger, Ute Curth, Joerg Langowski, Katalin Toth
SCIENTIFIC REPORTS
(2016)
Article
Cell Biology
Travis J. Gould, Katalin Toth, Norbert Muecke, Joerg Langowski, Alexandra S. Hakusui, Ada L. Olins, Donald E. Olins
Article
Cell Biology
Vladimir B. Teif, Jan-Philipp Mallm, Tanvi Sharma, David B. Mark Welch, Karsten Rippe, Roland Eils, Joerg Langowski, Ada L. Olins, Donald E. Olins
Article
Cell Biology
Travis J. Gould, Katalin Toth, Norbert Muecke, Joerg Langowski, Alexandra S. Hakusui, Ada L. Olins, Donald E. Olins
Article
Cell Biology
Vladimir B. Teif, Jan-Philipp Mallm, Tanvi Sharma, David B. Mark Welch, Karsten Rippe, Roland Eils, Joerg Langowski, Ada L. Olins, Donald E. Olins
Article
Multidisciplinary Sciences
Agata Pernus, Joerg Langowski
Article
Multidisciplinary Sciences
Norbert Muecke, Stefan Winheim, Holger Merlitz, Jan Buchholz, Joerg Langowski, Harald Herrmann
Article
Multidisciplinary Sciences
Alexander Gansen, Suren Felekyan, Ralf Kuhnemuth, Kathrin Lehmann, Katalin Toth, Claus A. M. Seidel, Joerg Langowski
NATURE COMMUNICATIONS
(2018)
Meeting Abstract
Biophysics
J. Krieger, J. Buchholz, A. Pernus, S. Burri, E. Charbon, J. Langowski
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2015)