Article
Microbiology
Morgan N. Price, Adam P. Arkin
Summary: To assist biologists in studying the functional residues of proteins, we developed two interactive web-based tools, SitesBLAST and Sites on a Tree. These tools identify homologs with known functional residues and show whether these residues are conserved. Additionally, Sites on a Tree visually displays how functional residues vary across a protein family. These tools provide valuable insights for predicting protein function and comparing key residues among similar proteins.
Article
Biochemical Research Methods
Chunmei Cui, Yuan Zhou, Qinghua Cui
Summary: The proposed functional divergence score (FDS) algorithm can effectively evaluate the functional differences between human and mouse orthologous genes, helping to uncover gene expression divergence and distinguish successful and failed drug targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Cell Biology
Narendra Pratap Singh, Robb Krumlauf
Summary: Gene duplication and divergence play a significant role in the generation of morphological diversity and emergence of novel features in vertebrates. Although genome sequencing has improved our understanding of gene and regulatory element evolution, progress in studying protein function conservation and divergence has been slow. Some studies have explored the functional evolution of related proteins, but understanding of protein function variation within gene families remains limited.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
James I. Mitchell-White, Thomas Stockner, Nicholas Holliday, Stephen J. Briddon, Ian D. Kerr
Summary: Members of the mammalian G subfamily of ATP-binding cassette transporters exhibit significant differences in substrate specificity, with ABCG2 playing a crucial role in multidrug resistance due to its wide substrate specificity. Analysis of conservation differences between members in a multiple sequence alignment of ABCG sequences from mammals reveals possible explanations for functional differences. Mapping sets of residues onto the 3D structure of ABCG2 illustrates a network of residues that may confer additional conformational flexibility, allowing for transport of a wider array of substrates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Sayoni Das, Harry M. Scholes, Neeladri Sen, Christine Orengo
Summary: FunSite is a machine learning predictor that identifies catalytic, ligand-binding, and protein-protein interaction functional sites in proteins. Its prediction performance outperforms other publicly available functional site prediction methods, and conserved residues in FunFams are enriched in functional sites.
Article
Biochemistry & Molecular Biology
Gaoqi Weng, Chao Shen, Dongsheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li, Jian Wu, Tingjun Hou
Summary: PROTACs, a novel therapeutic technology that selectively degrades targeted proteins, has achieved significant progress with two PROTACs in phase I clinical trials. However, the design of PROTACs remains challenging. PROTAC-DB, a web-based database, integrates structural information and experimental data of PROTACs, providing convenient querying and filtering tools for researchers.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Blaz Lupse, Nick Heise, Kathrin Maedler, Amin Ardestani
Summary: PHLPPs play a role in restoring beta-cell function and survival in diabetes. Their upregulation and activation are associated with beta-cell dysfunction, affecting the cell's ability to survive through control mechanisms.
CELL DEATH DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Yuka Okajima, Takashi Matsuzaka, Shun Miyazaki, Kaori Motomura, Hiroshi Ohno, Rahul Sharma, Takuya Shimura, Nurani Istiqamah, Song-iee Han, Yuhei Mizunoe, Yoshinori Osaki, Hitoshi Iwasaki, Shigeru Yatoh, Hiroaki Suzuki, Hirohito Sone, Takafumi Miyamoto, Yuichi Aita, Yoshinori Takeuchi, Motohiro Sekiya, Naoya Yahagi, Yoshimi Nakagawa, Tsutomu Tomita, Hitoshi Shimano
Summary: The research found various alterations in pancreatic islet vasculature in obese insulin-resistant mice and type 2 diabetic mice, including capillary dilation, increased blood flow, and decreased endothelial nitric oxide synthase activity. Amelioration of these abnormalities can be achieved through Elovl6 deficiency.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Biochemistry & Molecular Biology
Nikolai N. Sluchanko, Eugene G. Maksimov, Yury B. Slonimskiy, Larisa A. Varfolomeeva, Antonina Y. Bukhanko, Nikita A. Egorkin, Georgy Tsoraev, Maria G. Khrenova, Baosheng Ge, Song Qin, Konstantin M. Boyko, Vladimir O. Popov
Summary: This study presents the first crystal structures of OCP2 from cyanobacteria with different morphoecophysiological characteristics and provides a comprehensive comparison of their structure, spectroscopy, and function with OCP1, OCP3, and all-OCP ancestor. The structures enable the correlation of spectroscopic signatures with the effective number of hydrogen and the discovery of chalcogen bonds anchoring the ketocarotenoid in OCP, as well as the rotation of the echinenone's beta-ionone ring in the CTD. The structural data also helped rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Pharmacology & Pharmacy
Nuria Ardaiz, Celia Gomar, Marcos Vasquez, Shirley Tenesaca, Myriam Fernandez-Sendin, Claudia Augusta Di Trani, Virginia Belsue, Javier Escalada, Ulrich Werner, Norbert Tennagels, Pedro Berraondo
Summary: The fusion protein of insulin and apolipoprotein A-I prolonged the insulin half-life in circulation, accumulated in the liver, and reduced liver steatosis. The effects of apolipoprotein A-I are the main driver of these effects, making it a promising insulin derivative for the treatment of diabetic patients with fatty liver disease.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Plant Sciences
Li Yuan, Jingwen Pan, Shouhong Zhu, Yan Li, Jinbo Yao, Qiulin Li, Shengtao Fang, Chunyan Liu, Xinyu Wang, Bei Li, Wei Chen, Yongshan Zhang
Summary: SUN-domain containing proteins play crucial roles in various biological functions, with distinct characteristics observed between different subfamilies in plants. Specifically, the study highlights the functional divergence between SUN3 and SUN5 in cotton, with SUN5 playing an important role in reproductive development.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Gaoqi Weng, Xuanyan Cai, Dongsheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou
Summary: PROTAC-DB 2.0 is an updated online database that contains structural and experimental data about PROTACs. This second version expands the number of PROTACs to 3270 and provides additional information to aid in the understanding and design of PROTACs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Xiao-song Yu, Hong-run Wang, Fei-fan Lei, Rui-qi Li, Hui-peng Yao, Jin-bo Shen, Noor-ul Ain, Yi Cai
Summary: This study investigates the evolution of the PIP family in 23 plant species and the functional divergence in Arabidopsis. The results demonstrate that the PIP family has undergone functional divergence during evolution, leading to differential immune induction activity and root growth inhibition. Furthermore, transcriptomic and protein-protein interaction analysis reveal distinct functional differences in plant defense pathways between the two PIP subfamilies. This research provides new insights into the relationship between the structure and function of PIP and enhances our understanding of the connection between growth inhibition and immune responses.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Longxue Cai, Wenfeng Li, Renqing Zeng, Zuohong Cao, Qicai Guo, Qi Huang, Xianfa Liu
Summary: Valsartan exhibits neuroprotective effects in diabetic mice by ameliorating BBB dysfunction, which requires cellular CREB signaling in brain endothelial cells.
Article
Biotechnology & Applied Microbiology
Marco Y. Hein, Jonathan S. Weissman
Summary: Understanding the roles of viral and host factors in human cytomegalovirus infection was explored using CRISPR interference and nuclease screening. The study revealed how perturbations of critical host and viral factors can alter the progression and timing of infection. Results showed that perturbing host factors can impact the stage of infection, while perturbation of viral factors can lead to distinct infection trajectories.
NATURE BIOTECHNOLOGY
(2022)
Article
Neurosciences
Dhanisha J. Jhaveri, Imogen O'Keeffe, Gregory J. Robinson, Qiong-Yi Zhao, Zong Hong Zhang, Virginia Nink, Ramesh K. Narayanan, Geoffrey W. Osborne, Naomi R. Wray, Perry F. Bartlett
JOURNAL OF NEUROSCIENCE
(2015)
Article
Psychiatry
Chikako Ragan, Kalpana Patel, Janette Edson, Zong-Hong Zhang, Jacob Gratten, Bryan Mowry
SCHIZOPHRENIA RESEARCH
(2017)
Article
Multidisciplinary Sciences
Beben Benyamin, Ji He, Qiongyi Zhao, Jacob Gratten, Fleur Garton, Paul J. Leo, Zhijun Liu, Marie Mangelsdorf, Ammar Al-Chalabi, Lisa Anderson, Timothy J. Butler, Lu Chen, Xiang-Ding Chen, Katie Cremin, Hong-Weng Deng, Matthew Devine, Janette Edson, Jennifer A. Fifita, Sarah Furlong, Ying-Ying Han, Jessica Harris, Anjali K. Henders, Rosalind L. Jeffree, Zi-Bing Jin, Zhongshan Li, Ting Li, Mengmeng Li, Yong Lin, Xiaolu Liu, Mhairi Marshall, Emily P. McCann, Bryan J. Mowry, Shyuan T. Ngo, Roger Pamphlett, Shu Ran, David C. Reutens, Dominic B. Rowe, Perminder Sachdev, Sonia Shah, Sharon Song, Li-Jun Tan, Lu Tang, Leonard H. van den Berg, Wouter van Rheenen, Jan H. Veldink, Robyn H. Wallace, Lawrie Wheeler, Kelly L. Williams, Jinyu Wu, Xin Wu, Jian Yang, Weihua Yue, Zong-Hong Zhang, Dai Zhang, Peter G. Noakes, Ian P. Blair, Robert D. Henderson, Pamela A. McCombe, Peter M. Visscher, Huji Xu, Perry F. Bartlett, Matthew A. Brown, Naomi R. Wray, Dongsheng Fan
NATURE COMMUNICATIONS
(2017)
Article
Genetics & Heredity
Jacob Gratten, Qiongyi Zhao, Beben Benyamin, Fleur Garton, Ji He, Paul J. Leo, Marie Mangelsdorf, Lisa Anderson, Zong-Hong Zhang, Lu Chen, Xiang-Ding Chen, Katie Cremin, Hong-Weng Deng, Janette Edson, Ying-Ying Han, Jessica Harris, Anjali K. Henders, Zi-Bing Jin, Zhongshan Li, Yong Lin, Xiaolu Liu, Mhairi Marshall, Bryan J. Mowry, Shu Ran, David C. Reutens, Sharon Song, Li-Jun Tan, Lu Tang, Robyn H. Wallace, Lawrie Wheeler, Jinyu Wu, Jian Yang, Huji Xu, Peter M. Visscher, Perry F. Bartlett, Matthew A. Brown, Naomi R. Wray, Dongsheng Fan
Article
Genetics & Heredity
Fleur C. Garton, Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten, Anjali K. Henders, Zong-Hong Zhang, Janette Edson, Sarah Furlong, Sarah Morgan, Susan Heggie, Kathryn Thorpe, Casey Pfluger, Karen A. Mather, Perminder S. Sachdev, Allan F. McRae, Matthew R. Robinson, Sonia Shah, Peter M. Visscher, Marie Mangelsdorf, Robert D. Henderson, Naomi R. Wray, Pamela A. McCombe
MOLECULAR GENETICS & GENOMIC MEDICINE
(2017)
Article
Biochemistry & Molecular Biology
Esmi L. Zajaczkowski, Qjong-Yi Zhao, Zong Hong Zhang, Xiang Li, Wei Wei, Paul R. Marshall, Laura J. Leighton, Sarah Nainar, Chao Feng, Robert C. Spitale, Timothy W. Bredy
ACS CHEMICAL NEUROSCIENCE
(2018)
Article
Multidisciplinary Sciences
Zong Hong Zhang, Aik Aun Khoo, Ivana Mihalek
Article
Multidisciplinary Sciences
Zili Zhang, Jian Wang, Sifan Chen, Zhaoyu Wei, Zhengtu Li, Siwen Zhao, Wenju Lu
Article
Multidisciplinary Sciences
Zong Hong Zhang, Dhanisha J. Jhaveri, Vikki M. Marshall, Denis C. Bauer, Janette Edson, Ramesh K. Narayanan, Gregory J. Robinson, Andreas E. Lundberg, Perry F. Bartlett, Naomi R. Wray, Qiong-Yi Zhao
Article
Multidisciplinary Sciences
Ingrid S. Tarr, Emily P. McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong-Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
SCIENTIFIC REPORTS
(2019)
Article
Clinical Neurology
Min Chen, Qiong-Yi Zhao, Janette Edson, Zong Hong Zhang, Xiang Li, Wei Wei, Timothy Bredy, David C. Reutens
Article
Clinical Neurology
Alison L. Hogan, Natalie Grima, Jennifer A. Fifita, Emily P. McCann, Benjamin Heng, Sandrine Chan Moi Fat, Sharlynn Wu, Ram Maharjan, Amy K. Cain, Lyndal Henden, Stephanie Rayner, Ingrid Tarr, Katharine Y. Zhang, Qiongyi Zhao, Zong-Hong Zhang, Amanda Wright, Albert Lee, Marco Morsch, Shu Yang, Kelly L. Williams, Ian P. Blair
Summary: Our study confirmed the dysregulation of SFPQ as a common feature in the central nervous system of ALS patients. Additionally, we found significantly reduced SFPQ RNA expression in the central nervous system of patients. Furthermore, while nuclear depletion of SFPQ was not observed at the protein level, SFPQ-positive ubiquitinated protein aggregates were identified in patients' spinal motor neurons.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2021)
Article
Chemistry, Analytical
Na Qin, Longkai Liu, Deqing Huang, Bi Wu, Zonghong Zhang
Summary: This research introduces an efficient method to reduce network size and computational complexity by pruning channels and filters, making it feasible to deploy deep CNNs on resource constrained platforms and showing good application value in industrial production.
Proceedings Paper
Engineering, Industrial
Zonghong Zhang, Junjie Ma, Deqing Huang, Zhonghe Zhou, Zipeng Wan, Na Qin
Summary: A novel method combining Faster R-CNN and OC-CNN is proposed for fault diagnosis of the clamp part on train. The experimental results show that this method is effective and surpasses other combined methods.
PROCEEDINGS OF THE 2021 IEEE 16TH CONFERENCE ON INDUSTRIAL ELECTRONICS AND APPLICATIONS (ICIEA 2021)
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
D. Jhaveri, I. O'Keeffe, G. Robinson, Q-Y. Zhao, Z. H. Zhang, V. Nink, G. Osborne, N. Wray, P. Bartlett
JOURNAL OF NEUROCHEMISTRY
(2015)