Article
Toxicology
David Filipovic, Wenjie Qi, Omar Kana, Daniel Marri, Edward L. LeCluyse, Melvin E. Andersen, Suresh Cuddapah, Sudin Bhattacharya
Summary: The aryl hydrocarbon receptor (AhR) is a receptor that binds to environmental contaminants and its binding is tissue-specific and influenced by DNA sequences and chromatin context.
TOXICOLOGICAL SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Mason J. Appel, Scott A. Longwell, Maurizio Morri, Norma Neff, Daniel Herschlag, Polly M. Fordyce
Summary: New high-throughput biochemistry techniques provide quantitative kinetic and thermodynamic data for thousands of protein variants in parallel, requiring mutant libraries that are currently difficult to produce at needed scale and specificity. The approach presented in this study, uPIC-M, offers a scalable, rapid, and inexpensive solution for creating such libraries using recent advances in oligo synthesis, high-throughput sample preparation, and next-generation sequencing.
Article
Biochemistry & Molecular Biology
Nikolas Eggers, Peter B. Becker
Summary: Using a unique experimental system, this study explored the principles of DNA shape recognition and factor cooperativity in chromatin. By reconstituting chromatin on Drosophila genomes, the researchers identified the physiological binding profile of MSL2 through interaction with other factors and competition with non-functional sites. The results revealed novel aspects of target selection in a complex chromatin environment.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Microbiology
Yizhao Luan, Zehua Tang, Yao He, Zhi Xie
Summary: In this study, evidence was provided showing that coevolving residues in TF domains contribute to DNA binding specificity. It was demonstrated that the coevolving residues are more likely to coevolve with other TF subclass-determining sites and mutation of these coevolving residues could significantly reduce the stability of the TF-DNA complex. Overall, this study expands our understanding of the interaction among coevolving residues in TFs and their importance in transcriptional regulation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Benjamin Neveu, Chantal Richer, Pauline Cassart, Maxime Caron, Camille Jimenez-Cortes, Pascal St-Onge, Claire Fuchs, Nicolas Garnier, Stephane Gobeil, Daniel Sinnett
Summary: ETV6 transcriptional activity is crucial for blood cell development, but its regulatory network is still unknown. We identified genes that modulate ETV6 repressive transcriptional activity and revealed their role in cellular transformation.
Article
Multidisciplinary Sciences
Takuya Tsujino, Tomoaki Takai, Kunihiko Hinohara, Fu Gui, Takeshi Tsutsumi, Xiao Bai, Chenkui Miao, Chao Feng, Bin Gui, Zsofia Sztupinszki, Antoine Simoneau, Ning Xie, Ladan Fazli, Xuesen Dong, Haruhito Azuma, Atish D. D. Choudhury, Kent W. W. Mouw, Zoltan Szallasi, Lee Zou, Adam S. S. Kibel, Li Jia
Summary: Prostate cancer with BRCA1/2 mutations is sensitive to PARP inhibitors, but other DNA damage response gene alterations are not consistently predictive. In this study, CRISPR-Cas9 screens in BRCA1/2-proficient prostate cancer cells identify MMS22L deletion as a biomarker for PARP inhibitor hypersensitivity. Loss of CHEK2, unexpectedly, confers resistance to PARP inhibition through increased expression of BRCA2, but combination treatment with ATR inhibitor overcomes this resistance. These findings have implications for the use of PARP inhibitors and biomarkers in prostate cancer.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Concepcion Iniguez, Ulo Niinemets, Kristiina Mark, Jeroni Galmes
Summary: The kinetics parameters of Rubisco are crucial for understanding enzyme catalytic properties and for photosynthesis and crop modeling. Variability in measurements may arise from differences in methods and assay conditions, and corrections and recommendations are necessary to reduce this variability and allow for comparison of data obtained in different laboratories.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biology
Seiji N. Sugiman-Marangos, Shivneet K. Gill, Michael J. Mansfield, Kathleen E. Orrell, Andrew C. Doxey, Roman A. Melnyk
Summary: Diphtheria toxin (DT) is a bacterial exotoxin that plays a central role in toxinology. However, the origins and evolutionary adaptation of DT to human hosts are still unknown. In this study, the researchers determined the high-resolution structures of DT homologs from Streptomyces albireticuli and Seinonella peptonophila. Despite not being toxic to human cells, these DT homologs displayed significant structural similarities to DT. The researchers found that the functional determinants of host range extended beyond cellular receptor binding, and differences in pH-induced pore formation and cytosolic release played a major role in toxin delivery into cells. This work provides insights into the expanding family of DT toxins and the mechanisms of host adaptation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Genetics & Heredity
Biswajyoti Sahu, Tuomo Hartonen, Paivi Pihlajamaa, Bei Wei, Kashyap Dave, Fangjie Zhu, Eevi Kaasinen, Katja Lidschreiber, Michael Lidschreiber, Carsten O. Daub, Patrick Cramer, Teemu Kivioja, Jussi Taipale
Summary: Analysis of massively parallel reporter assays reveals that most transcription factor activity is additive and does not rely on specific TF-TF interactions. DNA sequences can determine gene expression, but the exact sequence determinants are still unknown. Machine learning models suggest that TFs act in an additive manner with weak grammar, and most enhancers increase gene expression without involving specific TF-TF interactions.
Article
Multidisciplinary Sciences
Pengcheng Zhang, Haochen Wang, Hanwen Xu, Lei Wei, Liyang Liu, Zhirui Hu, Xiaowo Wang
Summary: Designing promoters with desirable properties is crucial in synthetic biology. DeepSEED, an AI-aided framework that combines expert knowledge with deep learning techniques, has been successful in efficiently designing synthetic promoters and capturing implicit features in flanking sequences.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Vincentius Martin, Farica Zhuang, Yuning Zhang, Kyle Pinheiro, Raluca Gordan
Summary: This study investigates the cooperative DNA-binding patterns of transcription factors (TFs) using in vitro binding assays and machine-learning modeling. It finds that the distance and orientation between ETS1 sites are critical determinants of cooperative ETS1-ETS1 binding, while cooperative ETS1-RUNX1 interactions show more flexibility in distance and orientation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Barbara Gonzalez-Teran, Maureen Pittman, Franco Felix, Reuben Thomas, Desmond Richmond-Buccola, Ruth Huttenhain, Krishna Choudhary, Elisabetta Moroni, Mauro W. Costa, Yu Huang, Arun Padmanabhan, Michael Alexanian, Clara Youngna Lee, Bonnie E. J. Maven, Kaitlen Samse-Knapp, Sarah U. Morton, Michael McGregor, Casey A. Gifford, J. G. Seidman, Christine E. Seidman, Bruce D. Gelb, Giorgio Colombo, Bruce R. Conklin, Brian L. Black, Benoit G. Bruneau, Nevan J. Krogan, Katherine S. Pollard, Deepak Srivastava
Summary: This study identifies genetic variants associated with congenital heart disease (CHD) and prioritizes and screens these variants using protein interactome analysis, leading to the identification of potential causative genes for CHD.
Article
Biotechnology & Applied Microbiology
Francisco J. Sanchez-Rivera, Bianca J. Diaz, Edward R. Kastenhuber, Henri Schmidt, Alyna Katti, Margaret Kennedy, Vincent Tem, Yu-Jui Ho, Josef Leibold, Stella Paffenholz, Francisco M. Barriga, Kevan Chu, Sukanya Goswami, Alexandra N. Wuest, Janelle M. Simon, Kaloyan M. Tsanov, Debyani Chakravarty, Hongxin Zhang, Christina S. Leslie, Scott W. Lowe, Lukas E. Dow
Summary: Improved base editing libraries enable high-throughput functional analysis of single-nucleotide variants in cancer. A modular base-editing-activity sensor was developed to measure the editing efficiency and precision of thousands of sgRNAs paired with functionally distinct base editors. This comprehensive resource of sgRNAs can be used to study cancer-associated single nucleotide variants in cell and animal models.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Charles Bou-Nader, Ankur Bothra, David N. Garboczi, Stephen H. Leppla, Jinwei Zhang
Summary: The study reveals the selective recognition mechanism of S9.6 for hybrid double-stranded DNA and provides a framework for S9.6 protein engineering.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Xiang Zhao, Elizabeth M. Kolawole, Waipan Chan, Yinnian Feng, Xinbo Yang, Marvin H. Gee, Kevin M. Jude, Leah Sibener, Polly M. Fordyce, Ronald N. Germain, Brian D. Evavold, K. Christopher Garcia
Summary: This paper proposes a novel method to isolate TCR mutants that exhibit high activation signals coupled with low-affinity pMHC binding. Through this strategy, the mutant TCRs can enhance target killing potency while avoiding adverse cross-reactivity with off-target antigens.
Article
Biochemical Research Methods
Yinnian Feng, Xiang Zhao, Adam K. White, K. Christopher Garcia, Polly M. Fordyce
Summary: Adaptive immunity relies on T lymphocytes and T cell receptors (TCRs) to recognize peptides presented by major histocompatibility complex molecules (pMHCs). In vitro screening methods often fail to predict potent agonists in vivo because they lack biomechanical forces and test pMHCs at high densities. BATTLES is a technology that applies biomechanical force to initiate T cell triggering and allows high-throughput analysis of TCR-pMHC interactions in a physiological force-dependent manner.
Article
Nanoscience & Nanotechnology
Qitong Li, Jorik van de Groep, Adam K. White, Jung-Hwan Song, Scott A. Longwell, Polly M. Fordyce, Stephen R. Quake, Pieter G. Kik, Mark L. Brongersma
Summary: This article introduces a metasurface optofluidic platform that allows for dynamic control of light fields' intensity and spectral properties. By combining optofluidics and metasurface optics, new platforms for light field control are created. The researchers designed highly sensitive metasurface building blocks and used them to create flat optics inside microfluidic channels, manipulating the optical behavior by controlling the refractive index of the liquids. The results demonstrate the ability to tune the intensity and spectral properties of metasurface color pixels and the platform's automated control capability.
NATURE NANOTECHNOLOGY
(2022)
Article
Chemistry, Analytical
Margarita Khariton, Conor J. McClune, Kara K. Brower, Sandy Klemm, Elizabeth S. Sattely, Polly M. Fordyce, Bo Wang
Summary: Microfluidic droplet assays enable single-cell PCR and sequencing analyses at unprecedented scales. Encapsulating cells within picoliter double emulsion allows sorting droplets with commercially available FACS machines, making it possible to isolate single cells based on phenotypes of interest. However, sorting DE droplets with standard cytometers requires small droplets that can pass FACS nozzles. Therefore, this study overcame limitations by using a plate-based RT-PCR assay to ameliorate the inhibition and demonstrated one-step RT-PCR from single cells in 20 pL DE droplets with fluorescence quantifiable via FACS.
ANALYTICAL CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Lyndsay Mariah Stapleton, Justin Michael Farry, Yuanjia Zhu, Haley Joan Lucian, Hanjay Wang, Michael John Paulsen, Kailey Pearl Totherow, Gillie Agmon Roth, Kara Kimberly Brower, Polly Morrell Fordyce, Eric Andrew Appel, Yi-Ping Joseph Woo
Summary: Cardiovascular disease, particularly coronary artery disease, is the leading cause of death in the United States. This study investigates a photosynthetic oxygen delivery system using Synechococcus elongatus encapsulated in hydrogel microparticles to rescue myocardium following acute ischemia. The results demonstrate improved cell viability and left ventricular function, showing the potential of this approach for the treatment of myocardial ischemia.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2023)
Article
Multidisciplinary Sciences
Nicole DelRosso, Josh Tycko, Peter Suzuki, Cecelia Andrews, Adi Mukund, Ivan Liongson, Connor Ludwig, Kaitlyn Spees, Polly Fordyce, Michael C. Bassik, Lacramioara Bintu
Summary: Human gene expression is regulated by thousands of transcription factors and chromatin regulators. This study systematically measures the activity of over 100,000 protein fragments from these regulators and annotates previously unknown activation and repression domains. The research reveals the necessary residues for activation domain activity and identifies structures or motifs involved in repression. The findings provide valuable insights into the function of transcription factors and chromatin regulators and can aid in gene expression control and predictive modeling of effector domains.
Article
Biochemistry & Molecular Biology
Zheng Zuo, Timothy Billings, Michael Walker, Petko M. Petkov, Polly M. Fordyce, Gary D. Stormo
Summary: The human genome contains numerous zinc finger proteins (ZFPs) composed of long arrays of zinc fingers. Contradicting the standard ZFP recognition model, recent experiments have identified short motifs in ZFP binding sites. This study examines ZFY, CTCF, ZIM3, and ZNF343 to understand the reasons behind this and improve motif discovery algorithms. The study reveals the existence of 'dependent recognition' and downstream specificity modulation by upstream sites, and proposes an algorithm, ModeMap, to infer motifs and recognition models of ZIM3 and ZNF343.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jamin B. Hein, Hieu T. Nguyen, Dimitriya H. Garvanska, Isha Nasa, Thomas Kruse, Yinnian Feng, Blanca Lopez Mendez, Norman Davey, Arminja N. Kettenbach, Polly M. Fordyce, Jakob Nilsson
Summary: Investigating the specificity of phosphoprotein phosphatases (PPPs) has been challenging, but this study introduces a novel approach, MRBLE:Dephos, to determine phosphatase preferences. Using this method, the authors identified amino acid preferences of residues surrounding the dephosphorylation site for PP1 and PP2A-B55, and discovered key dephosphorylation sites during mitotic exit that are consistent with MRBLE:Dephos results.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Craig J. Markin, Daniel A. Mokhtari, Siyuan Du, Tzanko Doukov, Fanny Sunden, Jordan A. Cook, Polly M. Fordyce, Daniel Herschlag
Summary: Using high-throughput microfluidic enzyme kinetics, the impacts of single site mutations on the alkaline phosphatase PafA's affinity for two transition state analogs were measured. Active site and active-site-contacting residues had similar effects on catalysis and analog binding, while distal residues that reduced catalysis had little impact on binding and some even increased affinity. A model suggests that distal mutations alter the enzyme's conformation, accommodating larger analogs. These findings indicate the importance of both active site and distal residues in enzyme engineering.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Analytical
Margarita Khariton, Conor J. McClune, Kara K. Brower, Sandy Klemm, Elizabeth S. Sattely, Polly M. Fordyce, Bo Wang
Summary: Microfluidic droplet assays enable single-cell PCR and sequencing analyses at unprecedented scales. However, sorting small droplets for FACS poses challenges for molecular biology. To overcome this, we used a plate-based RT-PCR assay and showed that heat lysis can alleviate inhibition for most cell lines, allowing RT-PCR to proceed in low-picoliter volumes.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
David McIntyre, Ali Lashkaripour, Diana Arguijo, Polly Fordyce, Douglas Densmore
Summary: This article introduces two quality metrics for droplet generation: performance versatility and stability. These metrics were characterized using in silico simulation and experimental validation, and they improve the reproducibility and efficiency of droplet microfluidics, accelerating the development of sophisticated devices.
Review
Biochemical Research Methods
David McIntyre, Ali Lashkaripour, Polly Fordyce, Douglas Densmore
Summary: Microfluidics is a mature field with wide-ranging applications. However, the complexity of designing and controlling microfluidic devices hinders its adoption. Integration of machine learning with microfluidics can overcome these barriers and enable broader applications.
Article
Biochemical Research Methods
Suzanne G. K. Calhoun, Kara K. Brower, Vineeth Chandran Suja, Gaeun Kim, Ningning Wang, Alexandra L. McCully, Halim Kusumaatmaja, Gerald G. Fuller, Polly M. Fordyce
Summary: This article investigates the stability and size prediction of double emulsion droplets, providing a size parameterization model based on flow rate and buffer properties. The model is validated and shown to accurately predict droplet sizes. This research has the potential to simplify the development of novel screening-based biological assays using double emulsion droplets.
Meeting Abstract
Biophysics
Renee Hastings, Arjun Aditham, Polly Fordyce
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Connor A. Horton, Amr M. Alexandari, Michael G. Hayes, Julia M. Schaepe, Emil Marklund, Nilay Shah, Arjun K. Aditham, Avanti Shrikumar, Ariel Afek, William J. Greenleaf, Raluca Gordan, Julia Zeitlinger, Anshul Kundaje, Polly M. Fordyce
BIOPHYSICAL JOURNAL
(2022)