Article
Biotechnology & Applied Microbiology
Vindhya Mohindra, Labrechai Mog Chowdhury, Nishita Chauhan, Alisha Paul, Rajeev Kumar Singh, Basdeo Kushwaha, Rajesh Kumar Maurya, Kuldeep K. Lal, J. K. Jena
Summary: In this study, large-scale gill transcriptome analyses revealed differentially expressed genes (DEGs) in Tenualosa ilisha (Hilsa shad) in different salinity regions. The DEGs were mapped into various pathways, including focal adhesion and PI3K-Akt signaling pathways. The expression of certain osmoregulatory genes and other specific genes varied in different habitats. The results provide valuable information about the molecular mechanisms regulating water homeostasis in gills and potential bio-markers for adaptation to environmental changes.
MARINE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Marco Pedretti, Filippo Favretto, Francesca Troilo, Moira Giovannoni, Carolina Conter, Benedetta Mattei, Paola Dominici, Carlo Travaglini-Allocatelli, Adele Di Matteo, Alessandra Astegno
Summary: The direct interaction between Arabidopsis PCaP1 and CaM1 was investigated, with the myristoylated peptide enhancing the binding and altering the structure of CaM1. These findings suggest that the biological function of PCaP1 is related to the balance between myristoylation, Ca2+ ions, and CaM1.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Chengyang Huang, Wanqiong Huang, Pengchao Ji, Fuling Song, Tao Liu, Meiyang Li, Hongzhi Guo, Yongliang Huang, Cuicui Yu, Chuanxian Wang, Wenxiu Ni
Summary: The synthesized osmium(VI) nitrido complex has shown inhibitory effects on cervical, ovarian, and breast cancer cell lines, and modulates protein expression in HepG2 cells affecting mitochondrial function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Mustafa Coskun, Mehmet Koyuturk
Summary: Using node similarity-based convolution matrices in GCNs can significantly improve the link prediction performance of GCN-based embeddings. Experimental results in biomedical networks show that this approach can enhance the performance of link prediction.
Article
Chemistry, Applied
Ruixiang Ma, Zhantuo Lin, Yuehan Wu, Zhiming Gao, Bing Hu, Longquan Xu, Yapeng Fang, Katsuyoshi Nishinari
Summary: Heat-induced protein aggregates, including beta-lactoglobulin fibrils, nanoparticles, and worm-like aggregates, were studied to investigate the effects of disulfide bonds and surface hydrophobicity on their gastric digestion behavior. The results showed that surface hydrophobicity had a stronger influence on digestion extent compared to disulfide bonds, and the incorporation of polysaccharide could modulate the digestion extent linearly by decreasing both disulfide bond content and surface hydrophobicity.
Article
Biochemical Research Methods
Thao Vu, Elizabeth M. Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell P. Bowler, Farnoush Banaei-Kashani, Katerina J. Kechris
Summary: Biological networks provide a system-level understanding of underlying processes. In order to investigate the association between modules and variables of interest, a module summarization method that can explain the module's information and reduce dimensionality is needed. This article proposes NetSHy, a hybrid approach that incorporates topological properties to aid downstream analysis interpretation while reducing network dimensionality.
Article
Biochemistry & Molecular Biology
Mi Gyeong Jeong, Hyo Kyeong Kim, Gibbeum Lee, Hee Yeon Won, Da Hye Yoon, Eun Sook Hwang
Summary: TAZ is a key mediator of the Hippo signaling pathway and plays an important role in the pancreas. TAZ deficiency leads to shrinkage of pancreatic islet cells and decreased insulin production, causing hyperglycemia. TAZ and PDX1 work together in the pancreas to promote insulin production. TAZ deficiency impairs the differentiation of mesenchymal stem cells into insulin-producing cells, while TAZ recovery restores normal differentiation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Geng Tian, Shubin Wang, Jianhui Wu, Yanxia Wang, Xiutang Wang, Shuwei Liu, Dejun Han, Guangmin Xia, Mengcheng Wang
Summary: In this study, a drought tolerant gene TaWD40-4B.1 was identified in wheat through a genome-wide association study. The full-length allele TaWD40-4B.1(C) enhances drought tolerance and grain yield of wheat under drought, while the truncated allele TaWD40-4B.1(T) does not. TaWD40-4B.1(C) interacts with catalases, promotes their activities, and reduces H2O2 levels under drought.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Hyun-Myung Woo, Byung-Jun Yoon
Summary: MONACO is a novel and versatile network alignment algorithm that achieves highly accurate pairwise and multiple network alignments through iterative optimal matching of 'local' neighborhoods around focal nodes. Extensive performance assessments on real and synthetic networks, where the ground truth is known, show that MONACO consistently outperforms all other state-of-the-art network alignment algorithms in terms of accuracy, coherence, and topological quality of the aligned network regions. Despite the significantly enhanced alignment accuracy, MONACO remains computationally efficient and scales well with increasing size and number of networks.
Article
Biochemistry & Molecular Biology
Fu-Chun Xu, Mei-Juan Wang, Ya-Wei Guo, Jie Song, Wei Gao, Lu Long
Summary: This study discovered that cotton production is severely affected by salt stress, and identified SOS1 as a key gene for salt tolerance in cotton. It also identified SIP5 as a protein that interacts with SOS1 and negatively regulates salt tolerance in cotton. These findings provide a theoretical basis for elucidating the molecular mechanism of SOS1 and breeding salt-tolerant crops.
Review
Nutrition & Dietetics
Yanan Wang, Qing Liu, Seong-Gook Kang, Kunlun Huang, Tao Tong
Summary: Research indicates that cAMP plays a crucial role in metabolism and glucose homeostasis in various organs, while bioactive compounds in diet can influence diabetes pathogenesis by targeting cAMP signaling pathway.
Review
Immunology
Leila Abdelhamid, Xin M. Luo
Summary: The immune system plays a crucial role in defending against pathogens and maintaining homeostasis, but the impact of environmental factors like diet and hygiene on autoimmunity is not fully understood.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Plant Sciences
Jianping Liu, Wencheng Liao, Bo Nie, Jianhua Zhang, Weifeng Xu
Summary: Phosphorus is crucial for plant growth, and OsUEV1B plays a vital role in maintaining phosphate homeostasis in rice. Loss of OsUEV1B leads to Pi overaccumulation and toxicity in rice plants. Additionally, OsUEV1B interacts with OsVDAC1, which affects phosphate concentration and mitochondrial function in rice plants.
Article
Biochemistry & Molecular Biology
Idan Yakobov, Alysia Mandato, Lukas Hofmann, Kevin Singewald, Yulia Shenberger, Lada Gevorkyan-Airapetov, Sunil Saxena, Sharon Ruthstein
Summary: In this study, the dynamical changes of Escherichia coli CueR as a function of copper and DNA binding are measured using EPR spectroscopy. The results show that copper controls the activation of the transcription processes by initiating a series of dynamical changes over the protein.
Article
Biochemistry & Molecular Biology
Hang Zhou, Weikun Wang, Jiayun Jin, Zengwei Zheng, Binbin Zhou
Summary: This paper presents a comparative study of various graph neural networks for protein-protein interaction prediction. The experimental results show that hyperbolic graph neural networks tend to have a better performance than the other methods on the protein-related datasets.
Article
Biochemical Research Methods
Tara Walhart, Erin Isaacson-Wechsler, Kean-Hooi Ang, Michelle Arkin, Sharof Tugizov, Joel M. Palefsky
Article
Immunology
Andrew S. Mendiola, Jae Kyu Ryu, Sophia Bardehle, Anke Meyer-Franke, Kenny Kean-Hooi Ang, Chris Wilson, Kim M. Baeten, Kristina Hanspers, Mario Merlini, Sean Thomas, Mark A. Petersen, Alexander Williams, Reuben Thomas, Victoria A. Rafalski, Rosa Meza-Acevedo, Reshmi Tognatta, Zhaoqi Yan, Samuel J. Pfaff, Michael R. Machado, Catherine Bedard, Pamela E. Rios Coronado, Xiqian Jiang, Jin Wang, Michael A. Pleiss, Ari J. Green, Scott S. Zamvil, Alexander R. Pico, Benoit G. Bruneau, Michelle R. Arkin, Katerina Akassoglou
Article
Biochemistry & Molecular Biology
Joao Leandro, Susmita Khamrui, Hui Wang, Chalada Suebsuwong, Natalia S. Nemeria, Khoi Huynh, Moses Moustakim, Cody Secor, May Wang, Tetyana Dodatko, Brandon Stauffer, Christopher G. Wilson, Chunli Yu, Michelle R. Arkin, Frank Jordan, Roberto Sanchez, Robert J. DeVita, Michael B. Lazarus, Sander M. Houten
ACS CHEMICAL BIOLOGY
(2020)
Review
Pharmacology & Pharmacy
Vincent Blay, Bhairavi Tolani, Sunita P. Ho, Michelle R. Arkin
DRUG DISCOVERY TODAY
(2020)
Article
Biochemical Research Methods
May H. Abdel Aziz, Yao Fan, Lijun Liu, Mark M. Moasser, Haian Fu, Natalia Jura, Michelle R. Arkin
Summary: This study evaluated the use of Pichia pastoris as a host for expression of human kinases and showed that addition of the VLK domain improved expression and decreased aggregation of certain kinases. Some kinases were purified with good yield, purity, and comparable activity to commercially available versions.
PROTEIN EXPRESSION AND PURIFICATION
(2021)
Article
Microbiology
Rahul Tyagi, Christina A. Bulman, Fidelis Cho-Ngwa, Chelsea Fischer, Chris Marcellino, Michelle R. Arkin, James H. McKerrow, Case W. McNamara, Matthew Mahoney, Nancy Tricoche, Shabnam Jawahar, James W. Janetka, Sara Lustigman, Judy Sakanari, Makedonka Mitreva
Summary: 18 hits with anti-macrofilaricidal activity were identified, with azoles and aspartic protease inhibitors being prioritized for further study. These drugs showed activity against Onchocerca spp. as well, with the potential to identify selective drugs that prevent adverse events in co-infected individuals.
Article
Chemistry, Medicinal
Eline Sijbesma, Kenneth K. Hallenbeck, Sebastian A. Andrei, Reanne R. Rust, Joris M. C. Adriaans, Luc Brunsveld, Michelle R. Arkin, Christian Ottmann
Summary: The systematic discovery of functional fragments that bind to the composite interface of protein complexes is a critical step towards developing orthosteric stabilizers for protein-protein interactions (PPIs). By evaluating structure-activity relationships, it was found that covalent fragments engaging a relatively large and exposed binding pocket at the protein/peptide interface with a molecular glue mode of action can stabilize PPIs.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Marcus Y. Chin, Anand R. Patwardhan, Kean-Hooi Ang, Austin L. Wang, Carolina Alquezar, Mackenzie Welch, Phi T Nguyen, Michael Grabe, Anna Molofsky, Michelle R. Arkin, Aimee W. Kao
Summary: A novel genetically encoded fluorescent protein-based pH biosensor called FIRE-pHLy was designed to better understand lysosomal pH, enabling ratiometric quantification and targeting lysosomes with LAMP1. The biosensor reported lumenal pH between 3.5 and 6.0 with mTFP1 and enabled quantification of the alkalinizing response to bafilomycin Al in various cellular models. FIRE-pHLy is a specific, robust, and versatile lysosomal pH biosensor with broad applications in investigating pH dynamics in aging- and lysosome-related diseases and lysosome-based drug discovery.
Article
Biochemistry & Molecular Biology
Marcus Y. Chin, Kean-Hooi Ang, Julia Davies, Carolina Alquezar, Virginia G. Garda, Brendan Rooney, Kun Leng, Martin Kampmann, Michelle R. Arkin, Aimee W. Kao
Summary: The study aimed to identify small molecules that acidify lysosomal pH and molecular targets/pathways that regulate lysosomal pH. Using a new lysosomal pH biosensor, a high-throughput screening assay identified two compounds, OSI-027 and PP242, as top acidifying hits, which may be used to investigate potential therapeutic pathways for neurodegenerative diseases such as autophagy activation and lysosomal acidification.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Ziwen Jiang, Yu-Hsuan Kuo, Mengqi Zhong, Jianchao Zhang, Xin X. Zhou, Lijuan Xing, James A. Wells, Yanzhuang Wang, Michelle R. Arkin
Summary: Protein-protein interactions (PPIs) play crucial roles in cellular signaling and functions. Precise modulation of PPIs can help understand their roles in cellular events and be therapeutically valuable. In this study, an antibody fragment-based modulator for the PPI between p97 and its adaptor protein NSFL1C was developed, demonstrating its potential application in therapeutic interventions by disrupting specific intracellular PPIs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Yinyan Tang, Amber Kay, Ziwen Jiang, Michelle R. Arkin
Summary: Autophagy is a cellular process that degrades unwanted proteins and organdies by lysosomes. The interaction between LC3B and ATG4b is studied in this research, and it is found that LC3B-115, the core of LC3B, binds tightly to full-length ATG4b and inhibits its cleavage of pro-LC3B. The C-terminal tail of ATG4b contributes significantly to the binding affinity of LC3B-ATG4b interaction and wraps around the LC3B-ubiquitin core. These findings support a bipartite model for LC3B-ATG4b binding.
Article
Multidisciplinary Sciences
Megan L. Koleske, Gregory McInnes, Julia E. H. Brown, Neil Thomas, Keino Hutchinson, Marcus Y. Chin, Antoine Koehl, Michelle R. Arkin, Avner Schlessinger, Renata C. Gallagher, Yun S. Song, Russ B. Altman, Kathleen M. Giacomini
Summary: This study investigated the impact of variants in the SLC22A5 gene on the function of the carnitine transporter protein OCTN2 and created a predictive model. The results showed that most variants reduced carnitine transport, with some severely impairing function by at least 80%. Additionally, the study identified a major mechanism causing the loss of OCTN2 function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Ziwen Jiang, Yu-Hsuan Kuo, Michelle R. Arkin
Summary: Autophagy is a crucial process for the degradation of large cellular contents, and impaired autophagy can lead to pathological aggregation. This study developed a novel method for targeted degradation of protein aggregates and organelles in mammalian cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Julian R. Braxton, Chad R. Altobelli, Maxwell R. Tucker, Eric Tse, Aye C. Thwin, Michelle R. Arkin, Daniel R. Southworth
Summary: This study reports the structures of p97 protein bound to the UBXD1 adaptor and identifies UBXD1 as a potent ATPase inhibitor of p97. The structures, mutagenesis, and comparisons with other adaptors reveal how UBXD1 regulates the ATPase activity and structure of p97.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Marcus Y. Chin, Jether Amos Espinosa, Grace Pohan, Sarine Markossian, Michelle R. Arkin
Summary: Organelles play crucial roles in sustaining life and their dysfunction can lead to various diseases. The development of specifically targeted fluorescent probes is essential for accelerating drug discovery. Exploring organelle-specific morphology and dynamics, along with high-content analysis, can stimulate further development of probes and approaches for high-throughput screening of organelles.
CELL CHEMICAL BIOLOGY
(2021)