Review
Infectious Diseases
Yaru Wu, Zhenling Ma, Yanyan Zhang, Min Zhang, Xixi Shi, Menghao Zhang, Wenwen Zhang, Wei Liu
Summary: Cyclophilins (Cyps), a subgroup of peptidyl-prolyl cis-trans isomerases (PPIases) with a highly conserved domain, play important roles in various intracellular signaling pathways and are implicated in the development of diseases such as cardiovascular diseases, neurodegeneration, and cancer. Their involvement in viral infection as regulators of intercellular communication has attracted increasing attention, as viral proteins can target specific motifs of Cyps to manipulate infection outcomes.
JOURNAL OF INFECTION
(2022)
Article
Chemistry, Medicinal
Filippo Favretto, Eva Jimenez-Faraco, Carolina Conter, Paola Dominici, Juan A. Hermoso, Alessandra Astegno
Summary: This study characterized a conserved and a more divergent cyclophilin isoform from Toxoplasma gondii. The conserved isoform showed high activity and affinity for CsA, while the divergent isoform had low activity and was less sensitive to CsA inhibition. Structural studies revealed differences in the CsA-binding site between the two isoforms, suggesting distinct functions in the parasite.
ACS INFECTIOUS DISEASES
(2023)
Article
Oncology
Keisuke Maeda, Makoto Habara, Mitsuyasu Kawaguchi, Hiroaki Matsumoto, Shunsuke Hanaki, Takahiro Masaki, Yuki Sato, Hideyasu Matsuyama, Kazuki Kunieda, Hidehiko Nakagawa, Midori Shimada
Summary: FKBP51 and FKBP52 are key regulators of prostate cancer cell growth, with the inhibition of AR dimer formation serving as a promising treatment strategy for prostate cancer.
MOLECULAR ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Alexandra Born, Janne Soetbeer, Morkos A. Henen, Frauke Breitgoff, Yevhen Polyhach, Gunnar Jeschke, Beat Voegeli
Summary: Pin1 is a cell regulator with two domains. Ligand binding can change the conformation of these domains, thus affecting its catalytic site.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Huadi Shi, Fulan Zhong, Xiaoqiong Yi, Zhenyi Shi, Feiyan Ou, Yufang Zuo, Zumin Xu
Summary: A prognostic model based on 3 peptidyl prolyl cis-trans isomerase gene signatures was constructed for hepatocellular carcinoma patients. The model showed that patients in the high-risk score group had a worse prognosis, and the validation results were consistent with the training set. A nomogram incorporating clinical stage and risk score was established with a well-matched calibration curve.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Yi-Ting Wang, Wan-Yi Hsiao, Shao-Win Wang
Summary: Pin1 regulates the structure and function of eukaryotic RNA polymerase II through interaction with Rpb1 in response to oxidative stress, facilitating transcription elongation. Elevated Pin1 levels in cancer cells may help sustain survival under oxidative stress. These findings suggest a conserved function of Pin1 in cellular response to oxidative stress among eukaryotic cells with potential clinical implications.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Furyal Ahmed, Xin-Qiu Yao, Donald Hamelberg
Summary: This study compares the conformational dynamics of cyclophilin isoforms and identifies key dynamic residues in the gatekeeper 2 region that are essential for their catalytic activity. The highly conserved glycine residue (Gly80) is predicted to contribute to the local flexibility, which is further confirmed by molecular dynamics simulations on mutants (G80A) of CypE and CypA. The mutations lead to changes in flexibility and catalytic behavior of CypE and CypA, suggesting a loss of function.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Immunology
Zhao-Yi Wu, Anaamika Campeau, Chao-Hsien Liu, David J. Gonzalez, Masaya Yamaguchi, Shigetada Kawabata, Chieh-Hsien Lu, Chian-Yu Lai, Hao-Chieh Chiu, Yung-Chi Chang
Summary: Both PrsA isoforms play unique and overlapping roles in maintaining GAS proteome homeostasis and virulence-associated traits. Inactivation of both PrsA proteins in GAS leads to significant impairment in biofilm formation, host adherence, infection-induced cytotoxicity, and in vivo virulence in a murine soft tissue infection model. The concordance of proteomic and phenotypic data highlights the essential role of PrsA in full virulence of GAS.
Article
Multidisciplinary Sciences
Lulu Jiang, Pijush Chakraborty, Lushuang Zhang, Melissa Wong, Shannon E. Hill, Chelsea Joy Webber, Jenna Libera, Laura J. Blair, Benjamin Wolozin, Markus Zweckstetter
Summary: Alzheimer's disease and related tauopathies are characterized by misfolding and aggregation of the protein tau. This study demonstrates that the immunophilin FKBP12 regulates neuronal resilience by acting as a chaperone for monomeric tau. The study identifies the molecular factors involved in FKBP12's binding to tau and its influence on tau-induced neurotoxicity.
Article
Oncology
Muna Poudel, Poshan Yugal Bhattarai, Pratikshya Shrestha, Hong Seok Choi
Summary: IL-36 gamma plays a pivotal role in breast cancer by promoting the proliferation and transformation of epithelial cells through the activation of multiple signaling pathways and transcription factors. PIN1 is crucial in regulating IL-36 gamma-induced mammary gland tumorigenesis.
Article
Oncology
Binyan Zhao, Bailing Zhou, Kun Shi, Rui Zhang, Chunyan Dong, Daoyuan Xie, Lin Tang, Yaomei Tian, Zhiyong Qian, Li Yang
Summary: The combination of GalNAc-Pin1 siRNA with DP7-C nanoparticles and hydrogel enhances the stability and inhibitory effects of Pin1 siRNA, showing potential therapeutic efficacy in a liver cancer model.
Article
Immunology
Alisha Kellner, Patrick Cherubin, James K. Harper, Ken Teter
Summary: This study proposes that cis proline residues play a key role in the recognition of toxins by Hsp90, providing a new framework to understand the molecular basis for Hsp90 chaperone function and Hsp90-driven toxin translocation.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Weining Zhu, Linqing Xu, Xiaoxia Yu, Ying Zhong
Summary: A study reveals that the immunophilin CYP28 regulates the assembly and accumulation of photosystem II-light-harvesting complex II supercomplexes in plant chloroplasts. The lack of CYP28 results in accelerated leaf growth, earlier flowering time, and increased accumulation of high molecular weight PSII-LHCII supercomplexes. CYP28 likely alters the configuration of Lhcb6 through its PPIase activity to regulate the accumulation of PSII-LHCII supercomplexes.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Cell Biology
Yew Mun Lee, Deryn En-Jie Teoh, Kay Yeung, Yih-Cherng Liou
Summary: Pin1 plays a crucial role in various diseases, particularly in neurodegenerative diseases and cancer. Its conservation across different species highlights its importance, and using different Pin1 models may provide insights for disease therapeutics.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Agronomy
Ruiqi Zhang, Chuntian Lu, Xiangru Meng, Yali Fan, Jie Du, Runran Liu, Yigao Feng, Liping Xing, Petr Capal, Jaroslav Dolezel, Yiwei Wang, Huanqing Mu, Bingxiao Sun, Fu Hou, Ruonan Yao, Chuanxi Xiong, Yang Wang, Peidu Chen, Aizhong Cao
Summary: This study introgressed the novel wheat powdery mildew and stripe rust resistance genes Pm5V/Yr5V from Dasypyrum villosum and fine mapped them to a narrowed region in 5VS. The results showed that the Pm5V/Yr5V lines have the potential value to facilitate wheat breeding for disease resistance and do not incur a yield penalty in diverse wheat genetic backgrounds.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Tae-Yeon Kim, Eui-jeon Woo, Tae-Sung Yoon
Summary: Brazzein, a natural sweet protein, binds to taste receptors with stronger sweetness than sugar. Mutations of this protein affect its flavor and the study reveals the structural basis of the sweet mechanism induced by brazzein. The high-resolution structure data and docking model provide insights for understanding the flavor mechanism of sweet proteins.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Woo-Chan Ahn, Yan An, Kyung-Mo Song, Kwang-Hyun Park, Su-jin Lee, Byung-Ha Oh, Jong-Tae Park, Eui-Jeon Woo
Summary: Maltodextrin glucosidase (MalZ) is an important enzyme in the maltose utilization pathway in Escherichia coli. The crystal structure of MalZ reveals its substrate binding and hydrolysis mechanism, providing insights for protein engineering.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Geochemistry & Geophysics
Rudresh Dwivedi, Tanima Dutta, Yu-Chen Hu
Summary: The letter introduces a feature-based disease detection method L1-ELM, utilizing Kuan filtering for preprocessing and different feature computations. Experimental results demonstrate its superiority over all existing one-class classification algorithms in terms of optimal learning and better generalization.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Article
Engineering, Electrical & Electronic
Nitika Nigam, Tanima Dutta, Hari Prabhat Gupta
Summary: This paper addresses the challenging task of recognizing human actions in videos. It proposes a deep neural network architecture called FactorNet, which factors human actions and incorporates an attention mechanism to mitigate the influence of representation biases. Extensive experiments demonstrate the effectiveness of the proposed architecture and a new dataset called FactNet is designed for training and evaluation.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
(2022)
Article
Automation & Control Systems
Tanima Dutta, Sabyasachi Mohanty, Hari Prabhat Gupta
Summary: Digital oil painting is a revolutionary technique that simulates traditional oil painting brushes using digital brushes, allowing artists to repaint oil paintings quickly. A novel realistic technique was proposed with mathematical expressions to reduce time and space complexities. Prototypes were successfully developed on Android, Windows, and Ubuntu operating systems.
IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS
(2022)
Article
Computer Science, Information Systems
Swati Chopade, Hari Prabhat Gupta, Rahul Mishra, Aman Oswal, Preti Kumari, Tanima Dutta
Summary: This paper presents a sensor-based river water quality assessment system using deep neural network (DNN). The system estimates the water quality index (WQI) for labeling lab samples and uses automatic annotation technique to assign labels to sensory data instances. The labeled instances are then used to build a DNN classifier for predicting water quality. The system achieves high accuracy even with noisy labels.
IEEE INTERNET OF THINGS JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Simranjeet Singh Sekhon, Woo-Ri Shin, Sang Yong Kim, Dong-Seok Jeong, Wooil Choi, Bong-Keun Choi, Jiho Min, Ji-Young Ahn, Yang-Hoon Kim
Summary: Human cyclophilin A (hCypA) interacts strongly with the viral SARS-CoV-2 receptor-binding domain (RBD), blocking the binding of RBD to angiotensin-converting enzyme 2 (ACE2) receptor, thereby suppressing the entry of coronavirus into host cells. This suggests that hCypA may be a potential target for antiviral therapy.
BIOENGINEERING & TRANSLATIONAL MEDICINE
(2023)
Editorial Material
Engineering, Electrical & Electronic
Hari Prabhat Gupta, Uttam Ghosh, Biplab Sikdar, Tanima Dutta, Jan Faigl, Venkat R. R. Bhethanabotla, Kunal Mondal
Summary: Communicable diseases spread quickly through infectious mediums among people and animals, such as bacteria and viruses. The recent global outbreak of COVID-19 has motivated researchers to use smart sensor technologies to detect, prevent, and control the spread of communicable diseases. Smart sensors, including biosensors, wearable sensors, unmanned vehicles, and bedsheet sensors, collect real-time data on the transmissibility of diseases, which can be processed using advanced machine-learning techniques. The use of smart sensors helps facilitate more accurate diagnoses of communicable disease viruses.
IEEE SENSORS JOURNAL
(2023)
Article
Automation & Control Systems
Chitranjan Singh, Preti Kumari, Rahul Mishra, Hari Prabhat Gupta, Tanima Dutta
Summary: This article proposes an approach for securely processing a given IIoT task within an allowable response time. The approach uses game theory to estimate the fractions of the task to be containerized on different machines and maximizes the system utility.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2022)
Article
Automation & Control Systems
Rahul Mishra, Hari Prabhat Gupta, Ramakant Kumar, Tanima Dutta
Summary: Augmented intelligence is an innovative extension of artificial intelligence that enables human experts to take control of machine decisions and facilitates intelligent decision-making using IoT. This article presents a method to enhance the lifespan of unmanned aerial vehicle networks through augmented intelligence and evaluates it using existing datasets.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Shashanka Aroli, Eui-Jeon Woo, Balasubramanian Gopal, Umesh Varshney
Summary: UdgX removes uracil from uracil-containing DNA and forms a covalent bond with the resulting AP-DNA. It is structurally similar to family-4 UDGs (F4-UDGs) but unique in possessing a flexible R-loop (105KRRIH109). Mutations in UdgX reveal the role of specific amino acids in its enzymatic activity and substrate binding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Nitika Nigam, Tanima Dutta, Deepali Verma
Summary: Frequent falls among elderly adults and those with neurological disorders can cause injuries. Constant medical monitoring of individuals in the early stages of a neurological disorder is expensive. An uncertain action classification model is a cost-effective and scalable solution for regular monitoring of neurological decline and relapse frequency.
IEEE TRANSACTIONS ON COGNITIVE AND DEVELOPMENTAL SYSTEMS
(2023)
Article
Computer Science, Cybernetics
Aishwarya Soni, Tanima Dutta, Nitika Nigam, Deepali Verma, Hari Prabhat Gupta
Summary: This article presents a network model called SESANet for detecting faint text edges in noisy environments. It accurately localizes text in situations with poor contrast and illumination, and demonstrates superior performance on publicly available datasets.
IEEE TRANSACTIONS ON COMPUTATIONAL SOCIAL SYSTEMS
(2023)
Article
Computer Science, Cybernetics
Nitika Nigam, Tanima Dutta
Summary: Emotions and gestures are crucial in improving social intelligence and predicting human actions. Deep neural networks have become popular in recognizing visual actions, but classifying ambiguous actions remains challenging. This article proposes an attention-aware DNN called HAANet, which captures long-term temporal context to recognize actions in videos. HAANet extracts discriminative features of facial expressions and gestures in both spatial and temporal dimensions. The effectiveness of HAANet is demonstrated on benchmark datasets, and a new dataset called VALC is created to focus on the visual cues of human actions. HAANet outperforms other datasets in terms of accuracy.
IEEE TRANSACTIONS ON COMPUTATIONAL SOCIAL SYSTEMS
(2023)
Article
Computer Science, Hardware & Architecture
Preti Kumari, Rahul Mishra, Hari Prabhat Gupta, Tanima Dutta, Sajal K. K. Das
Summary: This paper proposes an energy-efficient smart metering system using Edge computing and LoRa technology, which compresses and transfers energy time series to reduce energy consumption and delay. The system utilizes deep learning compression model and optimization algorithm to achieve efficient energy transfer.
IEEE TRANSACTIONS ON SUSTAINABLE COMPUTING
(2022)
