Article
Plant Sciences
Yaxiu Xu, Jiaojiao Liu, Nannan Zang, Zepeng Yin, Aide Wang
Summary: This study identifies the mechanisms by which calcium regulates fruit ripening in apple fruit. It reveals that calcium affects multiple pathways involved in cell wall degradation, signaling and transport, protein degradation, and primary and secondary metabolisms. Phosphorylation and ubiquitination play important roles in these processes.
HORTICULTURAL PLANT JOURNAL
(2022)
Article
Biochemical Research Methods
Vincent Danna, Hugh Mitchell, Lindsey Anderson, Iobani Godinez, Sara J. C. Gosline, Justin Teeguarden, Jason E. McDermott
Summary: The goal of high-throughput data studies is to identify functional mechanisms underlying biological phenomena, which requires time-consuming evaluation of various statistical methods. The leapR package allows rapid assessment of biological pathway activity, facilitating integration of multisource data.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Tian Wang, Hao-Qi Wang, Bao Yuan, Guo-Kun Zhao, Yi-Ran Ma, Pei-Sen Zhao, Wen-Yin Xie, Fei Gao, Wei Gao, Wen-Zhi Ren
Summary: Proteomic and phosphoproteomic analyses were performed to investigate the changes in rat adenohypophysis after GnRH treatment. The results revealed proteins and phosphorylation sites related to FSH synthesis and secretion, providing valuable insights into the complex molecular mechanisms of GnRH-FSH regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Soo Young Cho, Heeyoun Hwang, Yun-Hee Kim, Byong Chul Yoo, Nayoung Han, Sun-Young Kong, Min-Jeong Baek, Kyung-Hee Kim, Mi Rim Lee, Jae Gwang Park, Sung-Sik Han, Woo Jin Lee, Charny Park, Jong Bae Park, Jin Young Kim, Sang-Jae Park, Sang Myung Woo
Summary: Through comprehensive analysis of genomic, transcriptomic, proteomic, and phosphoproteomic data from 102 iCC patients, three clinically supported subtypes were identified (stem-like, poorly immunogenic, and metabolism), and an organoid model was constructed for therapeutic testing. The ALDH1A1 inhibitor NCT-501 showed synergy with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. Dysregulations in oncometabolites were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype exhibited non-T-cell tumor infiltration. Integrated multiomics analysis reproduced the 3 subtypes and revealed heterogeneity in iCC.
Article
Biochemical Research Methods
Lili Blumenberg, Emily A. Kawaler, MacIntosh Cornwell, Shaleigh Smith, Kelly Ruggles, David Fenyo
Summary: Researchers use BlackSheep, a nonparametric description and differential analysis tool, to analyze molecules aberrantly enriched in small sample cohorts, complementing other differential expression analysis methods.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Oncology
Jing Hang, Hanqiang Ouyang, Feng Wei, Qihang Zhong, Wanqiong Yuan, Liang Jiang, Zhongjun Liu
Summary: In this study, we comprehensively analyzed the protein and phosphoprotein profiles of chordoma using proteomic and phosphoproteomic approaches. We identified aberrant expression of proteins and phosphorylation events in chordoma tumor tissues, and predicted the involvement of key kinases in the development of chordoma. We also demonstrated the therapeutic potential of targeting these kinases in inhibiting chordoma cell growth.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemical Research Methods
Huifang Zhu, Yongzhen Li, Jingyu Guo, Shuang Feng, Hong Ge, Chuansha Gu, Mengyao Wang, Ruicong Nie, Na Li, Yongxia Wang, Haijun Wang, Jiateng Zhong, Xinlai Qian, Guoyang He
Summary: This study used iTRAQ labeling proteomics and TMT labeling phosphoproteomics to identify differential proteins and phosphoproteins in colorectal cancer (CRC). The findings suggest that these proteins play important regulatory roles in tumorigenesis and are associated with biological and metabolic processes through binding to other molecules. Specifically, the up-regulation of the stem-loop binding protein (SLBP) in CRC cells promotes cell proliferation and migration. The integrated proteomic and phosphoproteomic analysis provides insights for diagnosing and treating CRC.
JOURNAL OF PROTEOMICS
(2023)
Article
Cell Biology
Yongjie Xu, Qiu Han, Chaofeng Ma, Yaling Wang, Pengpeng Zhang, Cencen Li, Xiaofang Cheng, Haixia Xu
Summary: Comprehensive proteomics analysis of sperm from Yorkshire and Duroc boars revealed differential expression of proteins and phosphorylated proteins related to crucial physiological functions such as sperm development, motility, and energy metabolism. Proteins involved in axonemal dynein complex assembly and sperm-egg recognition were found to be significantly higher in Duroc spermatozoa, indicating potential differences in sperm function between the two boar breeds.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Environmental Sciences
Juan Wang, Xiaojuan Wang, Conghui Zhang, Xiao Zhou
Summary: The study reveals the potential harm of microplastics to the human immune system. Microplastics in drinking water cause spleen damage and immune suppression in mice, potentially through modulation of protein expression and signaling pathways.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Multidisciplinary Sciences
Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
Summary: Protein phosphorylation is a well-known post-translational mechanism that plays a key role in cellular processes. While data-driven approaches have had limited success in revealing phosphosite functionality, using prior knowledge from literature-derived databases is a more suitable alternative. This study analyzed seven widely used databases to assess their suitability in providing functional insights into phosphoproteomics data, highlighting their relative strengths and weaknesses and providing guidance on how to best identify biological mechanisms in phosphoproteomic data.
Article
Biochemistry & Molecular Biology
Zoheir B. Demmouche, Jacques J. Tremblay
Summary: Leydig cells produce testosterone, a hormone essential for male sex differentiation and spermatogenesis. LH stimulates testosterone production by activating various kinases and transcription factors through increasing cAMP levels. AMPK, activated by AMP, potently represses steroidogenesis. The study identifies global changes in protein and phosphoprotein levels during both the stimulatory and inhibitory phases of steroidogenesis, providing new insights into the finely tuned processes of adequate steroid hormone production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Xi Zhang, Yang Liu, Zhen Zhang, Juan Tan, Junjun Zhang, Hao Ou, Jie Li, Zewen Song
Summary: This study investigated the mechanism of a novel angiogenesis inhibitor, anlotinib, against pancreatic cancer cells through multi-omics analyses, and constructed an anlotinib-related gene signature to identify a subgroup of pancreatic cancer patients who might benefit from anlotinib. The results showed that anlotinib exerted significant cytotoxicity on pancreatic cancer cells and had a profound inhibitory effect on ribosome, cell cycle, RNA metabolism, and lysosome.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Virginia Savy, Paula Stein, Min Shi, Carmen J. Williams
Summary: The study found that while there were subtle differences in calcium signaling in eggs following superovulation during parthenogenetic activation, there was no impact on the physiological calcium signaling at fertilization. This suggests that superovulation does not disrupt normal calcium signaling during fertilization, supporting its use for both clinical and experimental purposes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lianzhen Mao, Yunhua Dai, Yu Huang, Sha Yang, Hao Sun, Yao Zhou, Ying Sun, Bozhi Yang, Xuexiao Zou, Zhoubin Liu
Summary: The leaf is a vital plant organ linked to agricultural yields, and understanding leaf photosynthesis regulation can improve crop yield. This study analyzed the photosynthetic changes of pepper leaves under different light intensities, revealing significant effects on chlorophyll fluorescence and photosynthetic parameters. Proteins involved in photosynthesis and carbon fixation were differentially expressed, and phosphorylation levels varied under different light conditions. These findings provide new insights into studying pepper photosynthesis mechanisms under varying light intensities.
Article
Oncology
Kosuke Ogata, Shunsuke Takagi, Naoyuki Sugiyama, Yasushi Ishihama
Summary: Phosphoproteomics is crucial for understanding cell biology, but comprehensive analysis of the phosphoproteome is still lacking. Therefore, we introduced a new method to enrich a subset of the phosphoproteome and broaden the scope of analysis using in vitro kinase reactions. Our approach identified and quantified previously unobserved phosphopeptides and effectively profiled kinase inhibitors. This workflow can be easily adapted to target different subsets of the phosphoproteome and applied to various samples.
Article
Parasitology
Ana E. Garcia-Vedrenne, Anastasia C. E. Quintana, Andrea M. DeRogatis, Kayla Martyn, Armand M. Kuris, Ryan F. Hechinger
JOURNAL OF PARASITOLOGY
(2016)
Article
Parasitology
Ana E. Garcia-Vedrenne, Anastasia C. E. Quintana, Andrea M. DeRogatis, Christina M. Dover, Maribel Lopez, Armand M. Kuris, Ryan F. Hechinger
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2017)
Article
Chemistry, Analytical
Hongyue Ma, Jing Zhou, Hongbo Guo, Erxin Shang, Zhenhua Zhu, Uros Kuzmanov, Xiang Lv, Liuqing Di, Boyang Yu, Qinan Wu, Jinao Duan
ANALYTICA CHIMICA ACTA
(2018)
Article
Parasitology
Michelle L. Steinauer, Ana E. Garcia-Vedrenne, Sara B. Weinstein, Armand M. Kuris
JOURNAL OF PARASITOLOGY
(2019)
Article
Biochemical Research Methods
Lucas ZhongMing Hu, Florian Goebels, June H. Tan, Eric Wolf, Uros Kuzmanov, Cuihong Wan, Sadhna Phanse, Changjiang Xu, Mike Schertzberg, Andrew G. Fraser, Gary D. Bader, Andrew Emili
Article
Multidisciplinary Sciences
Sina Hadipour-Lakmehsari, Amine Driouchi, Shin-Haw Lee, Uros Kuzmanov, Neal I. Callaghan, Scott P. Heximer, Craig A. Simmons, Christopher M. Yip, Anthony O. Gramolini
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Chelsea L. Wood, Susanne H. Sokolow, Isabel J. Jones, Andrew J. Chamberlin, Kevin D. Lafferty, Armand M. Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia C. Buck, Andrea J. Lund, Ana E. Garcia-Vedrenne, Evan Fiorenza, Jason R. Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne P. Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau, Giulio A. De Leo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Fisheries
Kevin D. Lafferty, Ana E. Garcia-Vedrenne, John P. McLaughlin, Jasmine N. Childress, Marisa F. Morse, Christopher L. Jerde
Summary: At Palmyra Atoll, the eDNA signal on tidal sand flats was correlated with fish biomass density and detected 98%-100% of the expected species diversity. Although eDNA was found in different habitats, species associated with reefs contributed more eDNA to reef sites, while species linked to sand flats contributed more to sand-flat sites. The tidal effect did not disturb the eDNA signal in sand-flat habitats. At least 25 samples provided a coverage >97.5% in this diverse tropical marine system.
JOURNAL OF FISH BIOLOGY
(2021)
Article
Engineering, Biomedical
Uros Kuzmanov, Erika Yan Wang, Rachel Vanderlaan, Da Hye Kim, Shin-Haw Lee, Sina Hadipour-Lakmehsari, Hongbo Guo, Yimu Zhao, Meghan McFadden, Parveen Sharma, Filio Billia, Milica Radisic, Anthony Gramolini, Andrew Emili
NATURE BIOMEDICAL ENGINEERING
(2020)
Article
Ecology
Ana E. Garcia-Vedrenne, Chloe Orland, Kimberly M. Ballare, Beth Shapiro, Robert K. Wayne
ECOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Shin-Haw Lee, Sina Hadipour-Lakmehsari, Da Hye Kim, Michelle Di Paola, Uros Kuzmanov, Saumya Shah, Joseph Jong-Hwan Lee, Thomas Kislinger, Parveen Sharma, Gavin Y. Oudit, Anthony O. Gramolini
Article
Ecology
Meixi Lin, Ariel Levi Simons, Ryan J. Harrigan, Emily E. Curd, Fabian D. Schneider, Dannise V. Ruiz-Ramos, Zack Gold, Melisa G. Osborne, Sabrina Shirazi, Teia M. Schweizer, Tiara N. Moore, Emma A. Fox, Rachel Turba, Ana E. Garcia-Vedrenne, Sarah K. Helman, Kelsi Rutledge, Maura Palacios Mejia, Onny Marwayana, Miroslava N. Munguia Ramos, Regina Wetzer, N. Dean Pentcheff, Emily Jane McTavish, Michael N. Dawson, Beth Shapiro, Robert K. Wayne, Rachel S. Meyer
Summary: The study utilizes modern ecological models and community science to combine environmental DNA and Earth observations for a rapid snapshot of regional biodiversity patterns. Analysis of 278 samples reveals varying effects of environmental factors on different communities within ecosystems.
ECOLOGICAL APPLICATIONS
(2021)
Review
Surgery
Anthony Onde Morada, Sri Harshavardhan Senapathi, Amir Bashiri, Seungwoo Chai, Burt Cagir
Summary: This study aimed to elucidate the etiologies and development of malignancies at the ileostomy site. The study found that the indication and duration of the stoma were associated with the occurrence of malignant tumors. Regular screening is recommended for specific patients.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2022)
Article
Physiology
Farigol Hakem Zadeh, Allen C. T. Teng, Uros Kuzmanov, Paige J. Chambers, Allan R. Tupling, Anthony O. Gramolini
PHYSIOLOGICAL REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Jing Zhou, Hongyue Ma, Yuanyuan Wu, Xiang Lv, Jiajia Wang, Shengjin Liu, Dandan Li, Hengbin Wang, Yanqing Yan, Niancui Luo, Quan Li, Huiqin Xu, Qichun Zhang, Li Yu, Hongbo Guo, Uros Kuzmanov, Liuqing Di, Qinan Wu, Jinao Duan