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Biochemical Research Methods
Mehrdad Oveisi, Manu Shukla, Nogayhan Seymen, Masae Ohno, Yuichi Taniguchi, Sunil Nahata, Remco Loos, Ghulam J. Mufti, Robin C. Allshire, Stefan Dimitrov, Mohammad M. Karimi
Summary: iNucs is a user-friendly and efficient bioinformatics tool developed in Python for computing and visualizing nucleosome-nucleosome interactions. It uses standard pairs format input and is an important tool for deciphering chromatin organization.
Review
Chemistry, Multidisciplinary
Denise Liano, Ludovica Monti, Souroprobho Chowdhury, Federica Raguseo, Marco Di Antonio
Summary: This article discusses the research on G-quadruplex structures of DNA and their biological roles. The author challenges existing beliefs by discovering a human protein with high affinity and selectivity for intermolecular G-quadruplex structures, emphasizing the need for further study on the biological significance of these DNA structures. Furthermore, the potential role of G-quadruplex structures in neurodegenerative diseases is discussed.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jaegeon Joo, Sunghyun Cho, Sukbum Hong, Sunwoo Min, Kyukwang Kim, Rajeev Kumar, Jeong-Mo Choi, Yongdae Shin, Inkyung Jung
Summary: This study introduces a novel computational method to systematically characterize inter-chromosomal interactions using in situ Hi-C results. The research identifies two hub-like inter-chromosomal contacts associated with nuclear speckles and nucleoli, respectively, and finds that speckle-associated inter-chromosomal interactions are highly cell-type invariant with a marked enrichment of cell-type common super-enhancers (CSEs). The study also demonstrates the importance of MAZ binding in regulating speckle-associated inter-chromosomal contacts.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Lara Kern, Suhaib K. Abdeen, Aleksandra A. Kolodziejczyk, Eran Elinav
Summary: The gut microbiota, a complex ecosystem of microorganisms, involves various inter-bacterial interactions such as symbiosis, competition, and predation. These interactions play important roles in shaping microbiota diversity, niche formation, and responses to the host and environment.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Ecology
Michael J. Bottery, Jessica L. Matthews, A. Jamie Wood, Helle Krogh Johansen, Jon W. Pitchford, Ville-Petri Friman
Summary: The study found that multidrug-resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to Pseudomonas aeruginosa, but is ineffective against another antibiotic. The level of exposure protection against different carbapenems is determined by differences in antibiotic efficacy and inactivation rate.
Review
Plant Sciences
Masahito Nakano, Natsuki Omae, Kenichi Tsuda
Summary: Phytohormones play central roles in plant-microbe interactions, plant growth, and development. There are interconnections between phytohormone networks in plants and microbes, as they affect each other's metabolism and community composition. Further research is needed to understand the molecular mechanisms of phytohormone networks.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Xi Zha, Xiao-Hong Xu
Summary: Individuals of many species engage in intraspecific fighting to gain or defend critical resources, a behavior that is evolutionarily selected for in a species-, sex-, and environment-dependent manner. Recent studies in the house mouse model have identified a core neural circuit that controls male-male aggression.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Bryan D. Ryder, Irina Matlahov, Sofia Bali, Jaime Vaquer-Alicea, Patrick C. A. van der Wel, Lukasz A. Joachimiak
Summary: This study investigates the domain interactions of Hsp40 DnaJB8 and their impact on Hsp70 recruitment, revealing an interaction mechanism between the J-Domain and C-terminal domain that prevents Hsp70 binding, proposing a model for DnaJB8-Hsp70 recruitment.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
Allison M. Weis, June L. Round
Summary: IgA is the most abundant antibody at mucosal surfaces and plays a crucial role in neutralizing harmful toxins and regulating the composition and function of commensal microbiota. The interaction between IgA and the microbiota promotes homeostasis with the host to prevent disease.
CELL HOST & MICROBE
(2021)
Article
Biology
Wujie Zhang, Maimon C. Rose, Michael M. Yartsev
Summary: The goal of this study is to understand the neural relationship between socially interacting individuals. By studying bats engaged in spontaneous social interactions, the researchers found fast fluctuations of activity difference across brains which parallel slow activity covariation across brains. A computational model suggests that positive and negative feedback could explain various experimental observations regarding inter-brain neural relationship.
Article
Cell Biology
Chao Wei, Lumeng Jia, Xiaona Huang, Jin Tan, Mulan Wang, Jing Niu, Yingping Hou, Jun Sun, Pengguihang Zeng, Jia Wang, Li Qing, Lin Ma, Xinyi Liu, Xiuxiao Tang, Fenjie Li, Shaoshuai Jiang, Jingxin Liu, Tingting Li, Lili Fan, Yujie Sun, Juntao Gao, Cheng Li, Junjun Ding
Summary: This study reveals a novel role of CTCF in organizing long-range chromatin interactions, where CTCF phase separation mediated by RYBP promotes inter-A compartment interactions and enhances the self-renewal ability of embryonic stem cells.
Article
Computer Science, Information Systems
Fei Liu, Jing Liu, Zhiwei Fang, Richang Hong, Hanqing Lu
Summary: The study introduces a novel DenIII framework for visual question answering, which models dense inter- and intra-modality interactions by densely connecting all pairwise layers of the network. Extensive experiments confirm the effectiveness of the method, with DenIII achieving state-of-the-art or competitive performance on three publicly available datasets.
IEEE TRANSACTIONS ON MULTIMEDIA
(2021)
Review
Biochemistry & Molecular Biology
Kanak Joshi, Shanhui Liu, Peter S. J. Breslin, Jiwang Zhang
Summary: The TET family of proteins plays important roles in embryonic development and tissue generation by regulating gene expression. Interacting partner proteins and post-translational modifications regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are implicated in human diseases, particularly cancers.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biology
Yitong Li, Vijaya Kumar Balakrishnan, Michael Rowse, Cheng-Guo Wu, Anastasia Phoebe Bravos, Vikash K. Yadav, Ylva Ivarsson, Stefan Strack, Irina Novikova, Yongna Xing
Summary: This study demonstrates that PME-1 can regulate different families of PP2A holoenzymes and block substrate recognition. The high-resolution cryoelectron microscopy structure reveals the binding mode of PME-1 with the B56 regulatory subunit and the selective impact on PP2A-B56 holoenzymes. The findings uncover multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile activities.
Article
Geosciences, Multidisciplinary
Ido Marom, Tomer Toledo
Summary: There has been an increase in the frequency and intensity of disasters in recent decades, making evacuation and transportation plans crucial. A study of data collected after a WUI fire in Haifa, Israel, on November 24th, 2016, showed that individuals made multiple intermediate stops before evacuating or returning home. The research also revealed that households tend to gather together during disasters, with child pickup being a prominent activity involving a wider social circle beyond household members.
INTERNATIONAL JOURNAL OF DISASTER RISK REDUCTION
(2021)
Article
Multidisciplinary Sciences
Joseph H. A. Vissers, Samuel A. Manning, Aishwarya Kulkarni, Kieran F. Harvey
NATURE COMMUNICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Francesca Mattiroli, Joseph H. A. Vissers, Willem J. van Dijk, Pauline Ikpa, Elisabetta Citterio, Wim Vermeulen, Jurgen A. Marteijn, Titia K. Sixma
Article
Cell Biology
Joseph H. A. Vissers, Maarten van Lohuizen, Elisabetta Citterio
JOURNAL OF CELL SCIENCE
(2012)
Article
Immunology
Bart A. Westerman, A. Koen Braat, Nicole Taub, Marko Potman, Joseph H. A. Vissers, Marleen Blom, Els Verhoeven, Hans Stoop, Ad Gillis, Arno Velds, Wouter Nijkamp, Roderick Beijersbergen, Lukas A. Huber, Leendert H. J. Looijenga, Maarten van Lohuizen
JOURNAL OF EXPERIMENTAL MEDICINE
(2011)
Article
Immunology
Cesare Lancini, Paul C. M. van den Berk, Joseph H. A. Vissers, Gaetano Gargiulo, Ji-Ying Song, Danielle Hulsman, Michela Serresi, Ellen Tanger, Marleen Blom, Conchita Vens, Maarten van Lohuizen, Heinz Jacobs, Elisabetta Citterio
JOURNAL OF EXPERIMENTAL MEDICINE
(2014)
Article
Cell Biology
Joseph H. A. Vissers, Francesca Froldi, Jan Schroder, Anthony T. Papenfuss, Louise Y. Cheng, Kieran F. Harvey
Article
Oncology
Angela Mweempwa, Huiling Xu, Joseph H. A. Vissers, Richard W. Tothill, Andrew D. Pattison, Andrew P. Fellowes, David M. Thomas, Gary Richardson, Rodney J. Hicks, Sean M. Grimmond, Stephen B. Fox, Stephen J. Luen, Jayesh Desai, Benjamin J. Solomon
JCO PRECISION ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Francesco Nicassio, Nadia Corrado, Joseph H. A. Vissers, Liliana B. Areces, Steven Bergink, Jurgen A. Marteijn, Bart Geverts, Adriaan B. Houtsmuller, Wim Vermeulen, Pier Paolo Di Fiore, Elisabetta Citterio