Review
Microbiology
Constanze Kuhlisch, Adva Shemi, Noa Barak-Gavish, Daniella Schatz, Assaf Vardi
Summary: The cycling of major nutrients in the ocean is influenced by large-scale phytoplankton blooms, which are hot spots of microbial life. Microbial interactions, mediated by chemical crosstalk, play a crucial role in determining the type and outcome of these interactions. These interactions between microorganisms and algae are dependent on the environmental context.
NATURE REVIEWS MICROBIOLOGY
(2023)
Review
Endocrinology & Metabolism
Yan Meng, Zhengbo Tao, Siming Zhou, Wacili Da, Lin Tao
Summary: This study conducted a quantitative and qualitative analysis of melatonin research over the past 20 years using bibliometric methods, predicting future research trends. Findings showed that the United States had the highest number of publications in melatonin research, and future research hot spots are likely to focus on the structure and function of melatonin, clinical applications, and target-based drug design.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Lamei Huang, Zhixing Guo, Fang Wang, Liwu Fu
Summary: This review provides the latest understanding of fundamental aspects of KRAS, the relationship between KRAS mutations and tumor immune evasion, and new progress in targeting KRAS, particularly KRAS (G12C). The possible mechanisms of resistance to KRAS (G12C) inhibitors and potential combination therapies are also summarized, aiming to offer the best personalized treatment regimen with KRAS (G12C) inhibitors and achieve truly precise treatment.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
Review
Chemistry, Medicinal
Bin Zhao, Ajaybabu. V. V. Pobbati, Brian. P. P. Rubin, Shaun Stauffer
Summary: The Hippo signaling pathway is involved in cell proliferation and apoptosis, and the YAP/TAZ-TEAD interaction is an important target for cancer treatment. Direct small molecule disruptors targeting TEAD interfaces 2 and 3 pose challenges in inhibitor development.
Editorial Material
Medicine, General & Internal
Eric J. Rubin, Lindsey R. Baden, Stephen Morrissey
Summary: This article discusses the variations in infection rates and illness around the world and the implications for physicians.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Sagara N. S. Gurusinghe, Ben Oppenheimer, Julia M. Shifman
Summary: In this study, cold spots in protein-protein interactions (PPIs) are identified due to cavities and unfavorable charge interactions. Most cold spots are located in the periphery of the binding interface and are more frequent in non-cognate interactions compared to their cognate counterparts. Cold spots are also more frequent in homo-dimeric complexes compared to hetero-complexes. Glycines, glutamates, and arginines are the most frequent amino acids appearing at cold spot positions.
Article
Multidisciplinary Sciences
Heather Welch, Tyler Clavelle, Timothy D. White, Megan A. Cimino, Jennifer Van Osdel, Timothy Hochberg, David Kroodsma, Elliott L. Hazen
Summary: Illegal, unreported, and unregulated fishing causes significant economic losses, damage to aquatic life, and human rights violations. Vessel tracking data can help combat this issue, but the disabling of transponders reduces its effectiveness. A global dataset reveals that up to 6% of vessel activity is obscured, with hot spots of disabling located near Argentina, West African nations, and the Northwest Pacific. Disabling is most prevalent near transshipment hot spots and contested EEZ boundaries. The study also suggests a connection between disabling and hiding locations from competitors and pirates.
Article
Chemistry, Analytical
Yuhuan Gao, Jun Wang, Weina Wang, Tingting Zhao, Yanyun Cui, Pingping Liu, Shenghao Xu, Xiliang Luo
Summary: A simple and powerful Au NST@SiO2-based PEF probe with 20 symmetric hot spots was developed for highly sensitive intracellular miRNA imaging. By regulating the thickness of the silica shell, the distance between Au NSTs and fluorescent dyes was controlled, resulting in an optimal fluorescence enhancement (21-fold).
ANALYTICAL CHEMISTRY
(2021)
Article
Construction & Building Technology
Seok-Young Lim, Hyun-Jae Chang
Summary: Rapid growth in the information technology industry has led to exponential increase in data, requiring frequent upgrades of servers to high performance machines. Unfortunately, high-end servers and cooling systems consume significant energy. Hot spots at server inlets lower reliability and durability, as well as cooling efficiency, raising energy costs. This study introduces ventilation efficiency indices and analyzes airflow characteristics contributing to hot spots, finding that adjusting the vertical angle of server exhaust air can effectively suppress hot spots.
BUILDING AND ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Olivia Teixeira, Pedro Lacerda, Thamires Quadros Froes, Maria Cristina Nonato, Marcelo Santos Castilho
Summary: Assessment of target druggability is crucial in drug discovery, with FTMap providing raw data but requiring manual intervention for proper analysis. The DRUGpy plugin automates this process, enabling users to easily identify and characterize hot spots in protein targets. By analyzing the trypanothione reductases, DRUGpy has shown its utility in identifying druggable pockets and potential new avenues for drug design.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Review
Biotechnology & Applied Microbiology
Haoran Yu, Shuang Ma, Yiwen Li, Paul A. Dalby
Summary: Directed evolution is a powerful strategy to engineer protein properties, and hot spot prediction is crucial for producing smart libraries. Selection of hot spots based on sequence and structure allows for efficient generation of proteins with desired properties.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Environmental Sciences
Shan Zhao, Baoju Zhang, Xiaohui Sun, Leimin Yang
Summary: This paper reviews the pathways of nitrogen removal from hyporheic and riparian zones, with an emphasis on hot spots and hot moments, and outlines some research needs in this field.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Computer Science, Cybernetics
Argyris Constantinides, Christos Fidas, Marios Belk, Anna Maria Pietron, Ting Han, Andreas Pitsillides
Summary: The study suggests a novel cued-recall-based graphical authentication method that improves password security and memorability by leveraging users' sociocultural experiences. Results show that the approach influences users' password creation behavior, leading to stronger and more memorable passwords, but also introduces password guessing vulnerabilities for attackers with shared experiences.
INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES
(2021)
Article
Physiology
Tun Liu, Jiaxin Zhao, Xinyi Zhang, Yulin Wang, Wei Wang, Jidong Song
Summary: This paper presents a bibliometric study of publications related to the Wnt signaling pathway in bone to describe the current state of study and predict future outlooks.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andreia E. S. Cunha, Rui J. S. Loureiro, Carlos J. V. Simoes, Rui M. M. Brito
Summary: Influenza viruses cause significant morbidity and mortality through seasonal outbreaks and pandemics. Due to their high rate of evolution, yearly vaccine updates are required and antiviral drugs are less effective. Non-structural protein 1 (NS1) has emerged as a promising target for influenza antiviral therapy, as it plays essential roles in virus replication and pathogenesis. Through molecular dynamics simulations, we identified druggable pockets on NS1 that are partially conserved and co-localize with stable binding regions for PI3K and TRIM25, suggesting their potential as new targets for antiviral development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Noa Lahav, Shahar Rotem-Bamberger, Jamal Fahoum, Emma-Joy Dodson, Yahel Kraus, Reem Mousa, Norman Metanis, Assaf Friedler, Ora Schueler-Furman
Article
Chemistry, Medicinal
Ronen Gabizon, Nir London
JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Ronen Gabizon, Amit Shraga, Paul Gehrtz, Ella Livnah, Yamit Shorer, Neta Gurwicz, Liat Avram, Tamar Unger, Hila Aharoni, Shira Albeck, Alexander Brandis, Ziv Shulman, Ben-Zion Katz, Yair Herishanu, Nir London
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Biochemistry & Molecular Biology
Benika J. Pinch, Zainab M. Doctor, Behnam Nabet, Christopher M. Browne, Hyuk-Soo Seo, Mikaela L. Mohardt, Shingo Kozono, Xiaolan Lian, Theresa D. Manz, Yujin Chun, Shin Kibe, Daniel Zaidman, Dina Daitchman, Zoe C. Yeoh, Nicholas E. Vangos, Ezekiel A. Geffken, Li Tan, Scott B. Ficarro, Nir London, Jarrod A. Marto, Stephen Buratowski, Sirano Dhe-Paganon, Xiao Zhen Zhou, Kun Ping Lu, Nathanael S. Gray
NATURE CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Rambabu N. Reddi, Adi Rogel, Efrat Resnick, Ronen Gabizon, Pragati Kishore Prasad, Neta Gurwicz, Haim Barr, Ziv Shulman, Nir London
Summary: Chemical modifications of proteins can impact various aspects of protein function, but there are limited methods for site-specific labeling in cells. The CoLDR strategy presented in this study allows for the installation of functional tags on target proteins while preserving their activity, enabling a wide range of applications. This approach, which includes labeling various proteins and assessing protein activity in a native environment, contributes to the tools available in chemical biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Tomer Tsaban, Julia K. Varga, Orly Avraham, Ziv Ben-Aharon, Alisa Khramushin, Ora Schueler-Furman
Summary: Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have great impact on structural biology and beyond. This study demonstrates that AlphaFold2 can also be used for quick and accurate modeling of peptide-protein interactions. The results highlight the potential of AlphaFold2 in providing structural insight into a wide range of peptide-protein complexes.
NATURE COMMUNICATIONS
(2022)
Article
Urology & Nephrology
Alia Hassan, Yael E. E. Pollak, Rachel Kilav-Levin, Justin Silver, Nir London, Morris Nechama, Iddo Z. Z. Ben-Dov, Tally Naveh-Many
Summary: This study reveals that kidney failure leads to the loss of Pin1 activity in the parathyroid glands, resulting in increased production of PTH. Pin1 and KSRP phosphorylation, as well as the Pin1-KSRP-PTH mRNA axis, play important roles in secondary hyperparathyroidism.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Chemistry, Multidisciplinary
Roeland Vanhoutte, Marta Barniol-Xicota, Winston Chiu, Laura Vangeel, Dirk Jochmans, Steven De Jonghe, Hadeer Zidane, Haim M. Barr, Nir London, Johan Neyts, Steven H. L. Verhelst
Summary: The vulnerability of the modern society has been exposed by the COVID-19 pandemic, and it is crucial to have effective treatment options for infected individuals. We have designed a solid-phase synthesis route to create azapeptide activity-based probes for the SARS-CoV-2 main protease, which have shown to be potent inhibitors. These probes can be used to visualize the activity of the protease and the engagement of drugs in infected cells.
Editorial Material
Chemistry, Multidisciplinary
Julia K. Varga, Ora Schueler-Furman
Summary: Deep learning, led by DeepMind's Alphafold2, has brought revolutionary breakthroughs in structural biology, allowing generation of high-quality structural models for most known proteins and protein interactions. The next challenge is to utilize these models to understand protein binding, including partner identification and affinity. Chang and Perez propose an elegant approach, focusing on interactions involving short peptides and their receptors, where presenting both peptides to the receptor simultaneously allows Alphafold2 to predict the tighter binding peptide at the binding site. This simple yet effective idea demonstrates promising results.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Sayanika Banerjee, Julia K. Varga, Manoj Kumar, Guy Zoltsman, Shahar Rotem-Bamberger, Einav Cohen-Kfir, Michail N. Isupov, Rina Rosenzweig, Ora Schueler-Furman, Reuven Wiener
Summary: This study comprehensively investigates the activity of UFL1, its interaction with UFC1, and its relation to UBA5, revealing a novel regulatory mechanism.
Article
Chemistry, Multidisciplinary
Daniel S. Bejan, Sunil Sundalam, Haihong Jin, Rory K. Morgan, Ilsa T. Kirby, Ivan R. Siordia, Barr Tivon, Nir London, Michael S. Cohen
Summary: PARP16, a potential therapeutic target for cancer treatment, has poorly understood catalytic activity. This study describes the design of a selective PARP16 inhibitor and reveals that the catalytic activity of PARP16 regulates its solubility in response to nutrient stress.
Article
Genetics & Heredity
Tomer Tsaban, Doron Stupp, Dana Sherill-Rofe, Idit Bloch, Elad Sharon, Ora Schueler-Furman, Reuven Wiener, Yuval Tabach
Summary: Mapping co-evolved genes through phylogenetic profiling can reveal functional interactions and pathways in eukaryotes. By analyzing different clades, we found that functionally related genes exhibit distinct co-evolution patterns, highlighting the importance of modular co-evolution analysis. Our 'CladeOScope' method integrates information from multiple clades and genomes and can be accessed through a user-friendly web server.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Barr Tivon, Ronen Gabizon, Bente A. Somsen, Peter J. Cossar, Christian Ottmann, Nir London
Summary: The study introduces a computational pipeline, Rosetta CovPepDock, for successful docking of peptides with irreversible covalent bonds to protein receptors. Retrospective experiments showed a high success rate of 89% and 100% when docking from the native conformation. Additionally, by designing based on known non-covalent binders or protein-protein interfaces, the pipeline validated seven highly potent and selective irreversible peptide binders.
Article
Chemistry, Multidisciplinary
Aaron Morris, William McCorkindale, Nir Drayman, John D. Chodera, Savas Tay, Nir London, Alpha A. Lee
Summary: The research team used machine learning for novel compound design and synthesis route prediction, successfully identifying chemical scaffolds with antiviral activity. These findings are significant for the development of patent-free antiviral drugs.
CHEMICAL COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Ofrah Faust, Meital Abayev-Avraham, Anne S. Wentink, Michael Maurer, Nadinath B. Nillegoda, Nir London, Bernd Bukau, Rina Rosenzweig
