Article
Chemistry, Multidisciplinary
Yanan Liu, Dongliang Huo, Xufeng Zhu, Xu Chen, Ange Lin, Zhi Jia, Jie Liu
Summary: The study successfully synthesized a composite nano-catalyst based on ruthenium nanoframe, enhancing antibacterial activity through cascade catalysis and showing a promotion of wound healing in in vivo experiments.
Article
Thermodynamics
Youquan Xu, Anjan Tula, Xi Chen
Summary: This paper proposes a method that combines the selection of refrigerants with the optimization of the refrigeration process to design efficient refrigerants. By using properties databases of different refrigerants and using coefficient of refrigeration performance as the objective function, the optimal refrigerant and operating conditions can be obtained simultaneously.
INTERNATIONAL JOURNAL OF REFRIGERATION
(2023)
Article
Biochemistry & Molecular Biology
Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi
Summary: G2PDeep is an open-access web server that provides a deep-learning framework for quantitative phenotype prediction and genomic marker discovery. It allows researchers to create and train models through an interactive web interface, monitor training process, and compare model performance. Additionally, G2PDeep integrates multiple datasets, including the soybean nested association mapping data, for predictions of quantitative phenotypes and genomic markers.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Kaiqiao Li, Sijie Yao, Zhenyu Zhang, Biwei Cao, Christopher M. Wilson, Denise Kalos, Pei Fen Kuan, Ruoqing Zhu, Xuefeng Wang
Summary: In this paper, the authors introduce a new R package called "Xsurv" that utilizes modern GBDT training frameworks (XGB and LGB) to model right-censored survival outcomes. Through simulation experiments and the analysis of a melanoma methylation dataset, the authors demonstrate that Xsurv is a useful and computationally viable tool for screening prognostic candidate biomarkers.
Article
Microbiology
Cristina Rotoni, Marcio F. A. Leite, Agata Pijl, Eiko Eurya Kuramae
Summary: Rhizosphere microbial community composition is influenced by plant species and cultivar, and the genetic variability of plant cultivars has limited impact on microbial assembly composition. Different chrysanthemum cultivars select distinct rhizosphere microbiomes, and the selection is stronger for bacteria than for fungi. The genetic dissimilarity between cultivars explains a significant portion of the dissimilarity in bacterial selection, while fungal selection is not significantly linked to plant genetic dissimilarity.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xin Fan, Yang Gao, Fan Yang, Jian Liang Low, Lei Wang, Beate Paulus, Yi Wang, Andrej Trampuz, Chong Cheng, Rainer Haag
Summary: A bionanocatalyst Au@CuBCats containing dual-enzyme mimetics is synthesized to control glucose concentration and bacteria in diabetic ulcers, which demonstrates excellent antibacterial therapeutic efficacy.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Genetics & Heredity
Cameron B. Haas, James Ralston, Stephanie M. Fullerton, Aaron Scrol, Nora B. Henrikson
Summary: This study examines the implementation of automated family cascade genetic testing in electronic health records and finds limited bioinformatic support and non-technical barriers, including understanding of regulations, consent, and workflow.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Rinki Gupta, Mangal Singh, Ranjana Pathania
Summary: Antimicrobial resistance in bacterial pathogens is a global health issue. The lack of innovation in discovering new antibiotics remains a significant obstacle in addressing the AMR problem. Antibiotics currently target various essential components of bacterial cells, but there are several overlooked components in the bacterial cell envelope. This review focuses on antibacterial targets in the bacterial cell wall and discusses strategies for finding novel inhibitors, including high-throughput chemical genetic screening.
RSC MEDICINAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Yifan Zhang, Giovanni Gonzalez-Gutierrez, Katherine A. Legg, Brenna J. C. Walsh, Cristian M. Pis Diez, Katherine A. Edmonds, David P. Giedroc
Summary: The study reveals that the scavenging of reactive oxygen species by L-Ergothioneine (ET) in Streptococcus pneumoniae is facilitated by an ET uptake ATP-binding cassette transporter, EgtU. EgtU is highly conserved among Firmicutes and may contribute to antioxidant defenses in human pathogens.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Yifan Zhang, Giovanni Gonzalez-Gutierrez, Katherine A. Legg, Brenna J. C. Walsh, Cristian M. Pis Diez, Katherine A. Edmonds, David P. Giedroc
Summary: A protein encoded by the EgtU gene in Streptococcus pneumoniae has been found to specifically absorb ergothioneine, which is highly conserved in Firmicutes. This discovery provides important clues for studying the antioxidant mechanisms of human pathogens.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Yuewen Zhai, Yuying Ma, Bo Pang, Jinnan Zhang, Ying Li, Yalan Rui, Tian Xu, Yu Zhao, Zhiyu Qian, Yueqing Gu, Siwen Li
Summary: This study introduced a therapeutic regime to reinvigorate and activate the tumor immune microenvironment for enhancing the anti-tumor effect of PD-1 antibody. The biomimetic cascade targeting nanosystem, siRNA@PLOV, exhibited increased T cell infiltration and enhanced T cell cytotoxicity, particularly in combination with PD-1 antibody. Administering anti-PD-1 on the 5th day after siRNA@PLOV treatment showed the best tumor-killing performance and also presented a novel strategy for inducing vaccine effects to prevent tumor recurrence and improve prognosis.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Article
Limnology
Qiuwen Chen, Yuchen Chen, Jun Yang, Stephen C. Maberly, Jianyun Zhang, Jinren Ni, Gangsheng Wang, Daniele Tonina, Lin Xiao, Honghai Ma
Summary: This study found that water temperature, rather than the presence of dams, is the main factor influencing the geographical distribution of bacterial communities in cascade reservoirs. There are significant spatial differences in sediment bacterial communities within a reservoir, potentially forming hotspots for biogeochemical cycling. Unlike in deep lakes and deep single reservoirs, the bacterioplankton community composition in deep cascade reservoirs does not have distinctly layered features due to density-induced underwater currents and convection.
LIMNOLOGY AND OCEANOGRAPHY
(2021)
Article
Multidisciplinary Sciences
Jie Zeng, Yuzhi Hong, Ningqiu Zhao, Qianyu Liu, Weiwei Zhu, Lisheng Xiao, Weijie Wang, Miaomiao Chen, Shouqiang Hong, Liwen Wu, Yunxin Xue, Dai Wang, Jianjun Niu, Karl Drlica, Xilin Zhao
Summary: Recent research has shown that bacterial death can be achieved by activating ROS, and deficiencies in carbohydrate metabolism in certain genes can lead to pan-tolerance, impacting the response of bacteria to bactericidal agents like antibiotics and disinfectants and influencing antimicrobial treatment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
Zhanhong Hu, Hongcheng Li, Xiaohui Wang, Kifayat Ullah, Guoqiang Xu
Summary: Protein ubiquitylation plays critical roles in regulating various biological processes in eukaryotic cells with dysregulation leading to the onset of diseases; Identifying ubiquitylation sites is crucial for uncovering key ubiquitylation events associated with diseases and specific signaling pathways, and for understanding the biological functions of specific ubiquitylation events.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Siladitya Bandyopadhyay, Susmitnarayan Chaudhury, Dolly Mehta, Arati Ramesh
Summary: This study reports the discovery of iron-sensing RNA riboswitches named Sensei, which are present across bacterial phyla and exhibit high specificity for binding reduced iron. Iron binding by these riboswitches leads to conformational changes that enable genetic responses and increased translation of associated mRNA in vivo. The researchers also successfully engineered metal selectivity in riboswitches, altering their specificity for different metals.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Microbiology
David Burstein, Shirley Satanower, Michal Simovitch, Yana Belnik, Meital Zehavi, Gal Yerushalmi, Shay Ben-Aroya, Tal Pupko, Ehud Banin
Article
Genetics & Heredity
Megan Kofoed, Karissa L. Milbury, Jennifer H. Chiang, Sunita Sinha, Shay Ben-Aroya, Guri Giaever, Corey Nislow, Philip Hieter, Peter C. Stirling
G3-GENES GENOMES GENETICS
(2015)
Article
Cell Biology
Lee Zeev Peters, Ofri Karmon, Shir Miodownik, Shay Ben-Aroya
JOURNAL OF CELL SCIENCE
(2016)
Article
Multidisciplinary Sciences
Tal Keren-Kaplan, Lee Zeev Peters, Olga Levin-Kravets, Ilan Attali, Oded Kleifeld, Noa Shohat, Shay Artzi, Ori Zucker, Inbar Pilzer, Noa Reis, Michael H. Glickman, Shay Ben-Aroya, Gali Prag
NATURE COMMUNICATIONS
(2016)
Article
Genetics & Heredity
Ifat Lev, Keren Shemesh, Marina Volpe, Soumitra Sau, Nelly Levinton, Maya Molco, Shivani Singh, Batia Liefshitz, Shay Ben Aroya, Martin Kupiec
Article
Multidisciplinary Sciences
Hagit Bar-Yosef, Nora Vivanco Gonzalez, Shay Ben-Aroya, Stephen J. Kron, Daniel Kornitzer
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Ifat Lev, Keren Shemesh, Marina Volpe, Soumitra Sau, Nelly Levinton, Maya Molco, Shivani Singh, Batia Liefshitz, Shay Ben Aroya, Martin Kupiec
Editorial Material
Oncology
Shay Ben-Aroya, Erez Y. Levanon
Article
Cell Biology
Lilach Ben-Shimon, Viktoria D. Paul, Galit David-Kadoch, Marina Volpe, Martin Stuempfig, Eckhard Bill, Ulrich Muehlenhoff, Roland Lill, Shay Ben-Aroya
JOURNAL OF CELL SCIENCE
(2018)
Article
Biochemistry & Molecular Biology
Marina Volpe, Nelly Levinton, Nethanel Rosenstein, Gali Prag, Shay Ben-Aroya
Review
Ophthalmology
Nina Schneider, Yogapriya Sundaresan, Prakadeeswari Gopalakrishnan, Avigail Beryozkin, Mor Hanany, Eyal Banin, Shay Ben-Aroya, Dror Sharon
Summary: Inherited retinal diseases (IRDs) are a complex and heterogeneous group of visual impairments caused by pathogenic variants in numerous genes. The understanding of the genotype-phenotype correlations, inheritance patterns, hypomorphic alleles, and modifier genes associated with IRDs is challenging due to their unique characteristics. Advances in next-generation sequencing have facilitated the identification of novel IRD-related genes and variants. The Global Retinal Inherited Disease (GRID) dataset provides valuable information on the frequencies and complexities of pathogenic variants among 194 genes.
PROGRESS IN RETINAL AND EYE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Keren Friedman, Ofri Karmon, Uri Fridman, Yair Goldberg, Ophry Pines, Shay Ben-Aroya
Summary: Previous studies have shown that dysfunctional yeast proteasomes accumulate in the insoluble protein deposit (IPOD) and are prone to proteasome ubiquitination. However, our study reveals that only soluble proteasomes are targeted for autophagy, challenging the previous belief that sequestered proteasomes in IPOD are the substrates for proteaphagy. Moreover, the IPOD serves as an alternative pathway for the removal of inactive proteasomes that are not cleared by proteaphagy. This suggests that the relocalization of proteasomes to soluble aggregates is a crucial step in proteasome recycling through autophagy.
Article
Genetics & Heredity
Adi Avram-Shperling, Eli Y. Kopel, Itamar Twersky, Orshay Gabay, Amit Ben-David, Sarit Karako-Lampert, Joshua J. C. Rosenthal, Erez Levanon, Eli Eisenberg, Shay Ben-Aroya
Review
Biochemistry & Molecular Biology
Ofri Karmon, Shay Ben Aroya
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)