Article
Biochemistry & Molecular Biology
David Z. Bushhouse, Julius B. Lucks
Summary: Using the Clostridium beijerinckii pfl ZTP riboswitch as a model system, this study demonstrates that slowing down strand displacement can enable precise tuning of the riboswitch dynamic range. Various sequence barriers in the expression platforms of different Clostridium ZTP riboswitches were found to affect the dynamic range in different contexts. Additionally, the study shows that the same barriers can tune the dynamic range in a synthetic context, further elucidating how strand displacement can be manipulated to alter the riboswitch decision landscape.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Sofia Battaglia, Kevin Dong, Jingyi Wu, Zeyu Chen, Fadi J. Najm, Yuanyuan Zhang, Molly M. Moore, Vivian Hecht, Noam Shoresh, Bradley E. Bernstein
Summary: The use of targeted nanopore sequencing allowed researchers to analyze chromatin accessibility and DNA methylation on contiguous DNA molecules, leading to the identification of gene regulatory elements such as promoters, enhancers, insulators, and transcription factor binding sites. They also inferred relationships among dynamic elements within immune loci and determined the order of remodeling events during T cell stimulation. Additionally, they phased primary sequences and regulatory elements across the H19/IGF2 locus, revealing primate-specific features and a mechanism that overrides IGF2 imprinting in human cells.
Article
Optics
Thomas Pieter van Swieten, Jesse Merlijn Steenhoff, Auke Vlasblom, Ravi de Berg, Sam Pieter Mattern, Freddy Teunis Rabouw, Markus Suta, Andries Meijerink
Summary: Lanthanide-doped (nano)crystals play a crucial role in luminescence thermometry. By shifting the onset temperature of thermal equilibrium, the dynamic range of Boltzmann thermometers can be extended.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Juan Molina, Javier E. Escobar, Daniel Ramos, Eduardo Gil-Santos, Jose J. Ruz, Javier Tamayo, Alvaro San Paulo, Montserrat Calleja
Summary: Dynamic range quantifies the linear operation regime available in nanomechanical resonators. Nonlinearities can affect the response of nanowire resonators, but it is possible to achieve high values, up to 90 dB, through certain techniques.
Article
Computer Science, Information Systems
Ana Stojkovic, Jan Aelterman, Hiep Luong, Hans Van Parys, Wilfried Philips
Summary: A novel algorithm for detecting specular reflections and light sources in cinematic content is proposed in this study, which considers multiple features to improve the robustness of highlights detection. Experimental analysis shows that the algorithm outperforms conventional methods in both image data-sets and is suitable for LDR-to-HDR conversion with high quality reconstruction.
Article
Multidisciplinary Sciences
Sharon S. Newman, Brandon D. Wilson, Daniel Mamerow, Benjamin C. Wollant, Hnin Nyein, Yael Rosenberg-Hasson, Holden T. Maecker, Michael Eisenstein, H. Tom Soh
Summary: The current methods for quantifying the human plasma proteome are limited to a small range compared to the actual range. The authors propose a tuning approach for proximity-based assays that allows simultaneous quantification of multiple analytes across a wide concentration range. This method has the potential to greatly improve precision medicine by accurately describing patient physiology.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Unai Ortiz-Orruno, Ala Jo, Hakho Lee, Niek F. van Hulst, Matz Liebel
Summary: This study introduces a new off-axis k-space holography method that significantly boosts the achievable dynamic range to up to 110 dB by imaging the back-focal plane of a microscope to project the scattering signal of all particles onto all camera pixels. Validation of the platform with detection and quantitative sizing of metallic and dielectric particles demonstrates its effectiveness, along with the ability to correctly size particles made from different materials through independent signal calibrations.
Article
Chemistry, Analytical
Jianli Zhang, Alexander D. Wiener, Raymond E. Meyer, Cheuk W. Kan, David M. Rissin, Bharathi Kolluru, Christopher George, Carmen I. Tobos, Dandan Shan, David C. Duffy
Summary: This study presents methods to improve the quantification of digital bead assays (DBA), such as digital enzyme-linked immunosorbent assay (ELISA), which are widely used for highly sensitive protein measurement in clinical research and diagnostics. By changing the calculation method for the average number of enzymes per bead (AEB) and improving the determination of average product fluorescence intensity, the accuracy and robustness of DBA can be significantly improved.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Electrical & Electronic
Paul Nathan, Rebecca Manning, David M. Birch
Summary: A technique has been developed to compensate pressure readings from arrays of highly sensitive membrane-type pressure sensors for deflections caused by acceleration normal to the plane of the membrane using a single inertial measurement unit. By normalizing the fourth-order unsteady Kirchoff-Love equation, it can be shown that inertial body pseudoforces and applied surface pressure elicit a similar and additive response from the sensors. This proposed correction process reduces the maximum full-scale uncertainty of the measurements by as much as 50% by converting inertial effects into 'pseudopressures'.
IEEE SENSORS JOURNAL
(2021)
Article
Optics
Keiichiro Toda, Miu Tamamitsu, Takuro Ideguchi
Summary: The text discusses a supersensitive QPI technique that expands the dynamic range through a combination of wavefront shaping and dark-field QPI techniques. Experimental results show that this technique can improve the sensitivity of QPI and is useful for mid-infrared photothermal QPI.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Engineering, Multidisciplinary
Sherif M. Sharroush, Yasser S. Abdalla
Summary: This paper proposes three ultra-low current sources suitable for biomedical and implantable applications, with currents in the range of nanoamperes. One of the sources utilizes a modified version of the conventional Widlar MOS current source, employing a tunable subthreshold-region operated transistor as a controlled resistance. This current source is suitable for low-voltage and low-power applications. Additionally, two digitally controlled current sources (DCCSs)are proposed, which find wide-ranging applications in digital-to-analog converters, implantable microstimulators, and charge pumps. The three proposed current sources are quantitatively analyzed and verified through simulation using the 45 nm CMOS Predictive Technology Model (PTM) with a power-supply voltage, VDD, equal to 1 V.
AIN SHAMS ENGINEERING JOURNAL
(2023)
Article
Materials Science, Multidisciplinary
Chan Li, Haoyu Wang, Artemiy Dmitriev, Riccardo Maggiore, Haixing Miao, Sen Han
Summary: The Pound-Drever-Hall technique is widely used for laser frequency or optical cavity length stabilization. Our proposed method broadens its dynamic range, using the transmission power to improve resilience to noise and achieve a deterministic auto-lock even in the presence of large disturbances. However, this nonlinear extension is limited to an auto-lock for a previously locked state due to the requirement of accurate prior knowledge of the initial state.
RESULTS IN PHYSICS
(2021)
Article
Multidisciplinary Sciences
Lorenzo Rinaldi, Gregory Fettweis, Sohyoung Kim, David A. Garcia, Saori Fujiwara, Thomas A. Johnson, Theophilus T. Tettey, Laurent Ozbun, Gianluca Pegoraro, Michele Puglia, Blagoy Blagoev, Arpita Upadhyaya, Diana A. Stavreva, Gordon L. Hager
Summary: This study reveals that the interaction between a transcription factor and the cohesin loader NIPBL regulates gene activity, and this mechanism is achieved by promoting loop extrusion and long-range gene regulation at the chromatin level. Additionally, it is discovered that patients with cohesin mutations exhibit a reduced response to glucocorticoids.
Article
Multidisciplinary Sciences
E. D. Herbschleb, H. Kato, T. Makino, S. Yamasaki, N. Mizuochi
Summary: The authors demonstrate a non-adaptive algorithm to increase the sensing range while approaching the best sensitivity, outperforming the standard measurement concept in both sensitivity and range. They thoroughly explore this algorithm by simulation and discuss the T-2 scaling in the coherent regime, contrasting it with the T-1/2 of the standard measurement. This algorithm can be applied to any modulo-limited sensor.
NATURE COMMUNICATIONS
(2021)
Article
Optics
Fanfei Li, Shaohui Zhang, Lusong Li, Chenxu Xia, Jiankun Sun, Qun Hao
Summary: This paper proposes a method for high dynamics range 3D imaging in scenes with complex reflectivity, using a time-slicing strategy and phase unwrapping technique to achieve accurate measurement.
Article
Biochemistry & Molecular Biology
Marlies E. Oomen, Anders S. Hansen, Yu Liu, Xavier Darzacq, Job Dekker
Article
Biology
Claudia Cattoglio, Iryna Pustova, Nike Walther, Jaclyn J. Ho, Merle Hantsche-Grininger, Carla J. Inouye, M. Julius Hossain, Gina M. Dailey, Jan Ellenberg, Xavier Darzacq, Robert Tjian, Anders S. Hansen
Article
Biology
Matthew W. Parker, Maren Bell, Mustafa Mir, Jonchee A. Kao, Xavier Darzacq, Michael R. Botchan, James M. Berger
Article
Biochemistry & Molecular Biology
Anders S. Hansen, Assaf Amitai, Claudia Cattoglio, Robert Tjian, Xavier Darzacq
NATURE CHEMICAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Anna Sawicka, Gabriel Villamil, Michael Lidschreiber, Xavier Darzacq, Claire Dugast-Darzacq, Bjoern Schwalb, Patrick Cramer
Summary: In human cells, shortening CTD by half does not affect pre-mRNA synthesis and processing, but it does impact Pol II pausing, enhancer element transcription, and transcription activation after MAP kinase pathway stimulation. This suggests that a long CTD is necessary for efficient recruitment of Pol II to target genes for rapid activation.
Article
Cell Biology
Jonathan P. Karr, John J. Ferrie, Robert Tjian, Xavier Darzacq
Summary: This Perspective presents a new model for understanding how distal cis-regulatory elements communicate with promoters, diverging from the traditional enhancer-promoter looping paradigm. The model focuses on the coactivator p300 and offers a synthesis of the current literature to support its plausibility.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Dominik A. Herbst, Meagan N. Esbin, Robert K. Louder, Claire Dugast-Darzacq, Gina M. Dailey, Qianglin Fang, Xavier Darzacq, Robert Tjian, Eva Nogales
Summary: The cryo-EM structure of the human SAGA coactivator complex provides insights on its differences from yeast and the integration of a metazoan-specific splicing module, as well as reveals high-resolution details of the core and TRRAP modules.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Xavier Darzacq, Robert Tjian
Summary: Recent dynamic live-cell imaging experiments challenge our understanding of functional molecular interactions in vivo. While we have believed that functional biomolecular complexes are formed through stable assembly, new evidence suggests that function can be maintained even with rapid molecule exchange. This new perspective may significantly alter how we define the nature of molecular transactions critical for regulating cellular processes, and opens up new mechanistic options for interpreting essential biological processes such as gene regulation.
Article
Biology
Thomas G. W. Graham, John Joseph Ferrie, Gina M. Dailey, Robert Tjian, Xavier Darzacq
Summary: Single-molecule imaging is a powerful tool for studying biochemical processes in live cells, but tracking single molecules and detecting their interactions simultaneously remains challenging. This study describes a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which allows the detection of protein-protein interactions in live cells using two different labeled protein complexes in proximity.
Article
Biology
Alec Heckert, Liza Dahal, Robert Tijan, Xavier Darzacq
Summary: Single-particle tracking (SPT) is a powerful tool for studying molecular mechanisms of cellular regulation. However, there are technical limitations in interpreting SPT data for fast-diffusing proteins. Researchers have proposed methods based on Bayesian nonparametrics to address these limitations.
Article
Biology
Yu Chen, Claudia Cattoglio, Gina M. Dailey, Qiulin Zhu, Robert Tjian, Xavier Darzacq
Summary: The study has revealed the important role of intrinsically disordered regions (IDRs) in regulating the binding and diffusion behavior of transcription factors, providing insights into the mechanism of functional target site selectivity on chromatin.
Article
Genetics & Heredity
Tsung-Han S. Hsieh, Claudia Cattoglio, Elena Slobodyanyuk, Anders S. Hansen, Xavier Darzacq, Robert Tjian
Summary: Short-term maintenance of most gene expression and enhancer-promoter interactions does not require CTCF, Cohesin, WAPL, or YY1, but Cohesin may facilitate transcription factor binding to targets more efficiently.
Review
Biochemistry & Molecular Biology
Liza Dahal, Nike Walther, Robert Tjian, Xavier Darzacq, Thomas G. W. Graham
Summary: The interactions between molecules determine their movement. Single-molecule tracking (SMT) provides a unique means to observe the dynamic interactions of biomolecules within live cells. This article discusses the working principle of SMT, its implications in molecular biology, and how it has revolutionized our understanding of nuclear processes. The article also highlights the current limitations of SMT and explores new technical advancements that aim to overcome these limitations.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Biochemistry & Molecular Biology
Samuel Collombet, Isabell Rall, Claire Dugast-Darzacq, Alec Heckert, Aliaksandr Halavatyi, Agnes Le Saux, Gina Dailey, Xavier Darzacq, Edith Heard
Summary: The authors demonstrate that the disappearance of RNA polymerase II (RNAPII) from the inactive X chromosome territory is not caused by biophysical compartmentalization, but rather due to the loss of RNAPII bound fraction on chromatin. They show that RNAPII freely accesses the Xist territory during the initiation of X chromosome inactivation (XCI), indicating that the exclusion of RNAPII is not a consequence of physical compartmentalization. These findings highlight the importance of actively transcribing RNAPII in the regulation of gene silencing during XCI.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biology
Lorenzo Costantino, Tsung-Han S. Hsieh, Rebecca Lamothe, Xavier Darzacq, Douglas Koshland
