Article
Biochemical Research Methods
Leonie Schuermeyer, Kirsten Schorning, Joerg Rahnenfuehrer
Summary: An important problem in toxicology is the simultaneous inference of concentration-response relationships in gene expression data. The choice of experimental design and the set of concentrations used for observations greatly affect the quality of inference. In this study, we propose efficient designs for simultaneous inference and use D-optimality criterion and K-means procedure for clustering support points.
BMC BIOINFORMATICS
(2023)
Article
Environmental Sciences
Mary Jean See, David C. Bencic, Robert W. Flick, Jim Lazorchak, Adam D. Biales
Summary: This study characterized the VTG protein in male fathead minnow mucus compared to plasma and liver mRNA. The results showed that the induction kinetics of VTG protein concentration in mucus and plasma were similar, with a significant increase detected after 2 days of exposure in the mucus-based assay and after 7 days in the plasma-based assay.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Cell Biology
Yan Liang, Kota Kaneko, Bing Xin, Jin Lee, Xin Sun, Kun Zhang, Gen-Sheng Feng
Summary: This study analyzed single-cell transcriptomes of mouse livers and identified hepatocyte heterogeneity and the zonated metabolic functions. It also discovered a group of macrophages with a hybrid phenotype that may play a role in sinusoidal construction and Treg-cell function. The comprehensive atlas provided by this study is important for understanding liver development, metabolism, and disease.
DEVELOPMENTAL CELL
(2022)
Article
Multidisciplinary Sciences
Johanna Beil, Juliane Perner, Lena Pfaller, Marie-Apolline Gerard, Alessandro Piaia, Arno Doelemeyer, Adi Wasserkrug Naor, Lori Martin, Aline Piequet, Valerie Dubost, Salah-Dine Chibout, Jonathan Moggs, Remi Terranova
Summary: The possibility of adaptive inherited effects in mammals due to ancestral environmental exposure has long been debated. This study comprehensively investigates the transgenerational effects of exposure to a hepatotoxicant in rats and finds no morphological replication of enhanced wound healing response. However, transcriptional effects suggest transmission at the molecular level, although the functional relevance remains unclear.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Chanchan Xu, Zeyu Li, Jianbo Wang
Summary: Understanding the cellular mechanisms of invasive plant adaptation to excessive cadmium is important for phytoremediation strategies. This study found tissue-specific gene expression differences in the roots and leaves of Solidago canadensis exposed to cadmium stress. Root adaptation involved up-regulation of genes encoding molecular chaperones and induction of antioxidants, while leaf exposure increased genes related to secondary metabolism and decreased photosynthetic functions. Candidate gene modules linked to physiological traits were also identified.
Article
Multidisciplinary Sciences
Natalie M. Clark, Trevor M. Nolan, Ping Wang, Gaoyuan Song, Christian Montes, Conner T. Valentine, Hongqing Guo, Rosangela Sozzani, Yanhai Yin, Justin W. Walley
Summary: This study analyzed the BR signaling in Arabidopsis by integrating multiple omics datasets and inferring networks, identifying a BR-regulated transcription factor BRONTOSAURUS that affects cell division in roots. The research provides insights into the molecular signaling events during BR response through integrative network analysis applied to multi-omic data.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Bethany M. Moore, Yun Sun Lee, Peipei Wang, Christina Azodi, Erich Grotewold, Shin-Han Shiu
Summary: The modeling and experimental validation of transcriptional response to wounding and jasmonic acid identified temporal cis-regulatory codes and new regulatory sequences important for wound response. The study provides a global predictive model for wound response and highlights the significance of regulatory factors and open chromatin regions in different types of wound response.
Article
Agriculture, Dairy & Animal Science
Qian-Qian Li, Jing Zhang, Hong-Yang Wang, Su-Fang Niu, Ren-Xie Wu, Bao-Gui Tang, Qing-Hua Wang, Zhen-Bang Liang, Yan-Shan Liang
Summary: This study investigated the transcriptomic response of Trachinotus ovatus liver to high-temperature stress. Differential expression and STEM analyses identified high-temperature-related genes and pathways related to protein balance, hypoxia adaptation, and energy metabolism. The findings suggest the importance of protein dynamic balance and function, hypoxia adaptation, and energy metabolism transformation in response to acute heat stress, providing insights for the selection and breeding of heat-tolerant cultivars and the high-quality development of aquaculture.
Article
Multidisciplinary Sciences
Shizhe Yu, Haoren Wang, Lingpeng Yang, Yingxue Yan, Qiang Cai, Duo Ma, Long Jiang, Zehai Gao, Zhiyong Yu, Zongping Xia
Summary: The comprehensive study of the spatial-cellular anatomy of the human liver is crucial for understanding the cellular origins of liver disease. In this study, spatial transcriptomics were conducted on normal human liver tissue sections, providing detailed transcriptional information on liver zonation. A total of 6581 high-quality spots from normal livers were analyzed, mainly consisting of hepatocytes, which were classified into four sub-groups. These data serve as a reliable reference for studying the spatial heterogeneity of liver lobules.
Article
Multidisciplinary Sciences
Philipp Klein, Stefan M. Kallenberger, Hanna Roth, Karsten Roth, Thi Bach Nga Ly-Hartig, Vera Magg, Janez Ales, Soheil Rastgou Talemi, Yu Qiang, Steffen Wolf, Olga Oleksiuk, Roma Kurilov, Barbara Di Ventura, Ralf Bartenschlager, Roland Eils, Karl Rohr, Fred A. Hamprecht, Thomas Hoefer, Oliver T. Fackler, Georg Stoecklin, Alessia Ruggieri
Summary: This study elucidated the molecular mechanism of stress granules formation by integrating quantitative experiments and mathematical modeling. The study revealed that the stress response is controlled by a stochastic switch, with key elements including cooperative activation of PKR, ultrasensitive response of SG formation to eIF2 alpha phosphorylation, and negative feedback via GADD34. Furthermore, the study identified GADD34 mRNA levels as a molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.
Article
Microbiology
James W. Conrad, Valerie J. Harwood
Summary: This study reveals that sewage can significantly increase the density of Vibrio vulnificus populations and affect the transcription of genes associated with virulence, suggesting an increased risk of V. vulnificus infections.
MICROBIOLOGY SPECTRUM
(2022)
Article
Fisheries
Ljudevit Luka Bostjancic, Caterina Francesconi, Lena Bonassin, Sandra Hudina, Romana Gracan, Ivana Maguire, Christelle Rutz, Ana Beck, Ana Dobrovic, Odile Lecompte, Kathrin Theissinger
Summary: Alien invasive species are one of the main drivers of biodiversity loss in freshwater ecosystems. In Europe, the pathogen Aphanomyces astaci is considered one of the most problematic invasive species, as its introduction has severely reduced European freshwater crayfish stocks, particularly the noble crayfish population. However, the temporal dynamics of the noble crayfish immune response during Ap. astaci infection remains poorly understood.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle
Summary: MEFISTO is a flexible and versatile toolbox for modeling high-dimensional data with spatial or temporal dependencies, enabling spatio-temporally informed dimensionality reduction, interpolation, and separation of smooth and non-smooth patterns of variation. It can also integrate underlying patterns of variation in multiple related datasets in a data-driven manner.
Article
Cell Biology
Junliang Kuang, Jieyi Wang, Yitao Li, Mengci Li, Mingliang Zhao, Kun Ge, Dan Zheng, Kenneth C. P. Cheung, Boya Liao, Shouli Wang, Tianlu Chen, Yinan Zhang, Congrong Wang, Guang Ji, Peng Chen, Hongwei Zhou, Cen Xie, Aihua Zhao, Weiping Jia, Xiaojiao Zheng, Wei Jia
Summary: A new treatment for alleviating NAFLD has been discovered, which involves inhibiting intestinal FXR and upregulating hepatic CYP7B1 through a group of gut microbiota-modified bile acids. These bile acids can also increase the abundance of probiotic species and enhance lipid catabolism through the activation of PPARα signaling pathway, leading to an upregulation of hepatic FXR.
Article
Multidisciplinary Sciences
Nimish Godbole, Iiris Nyholm, Maria Hukkinen, Joseph R. Davidson, Athanasios Tyraskis, Jouko Lohi, Paivi Heikkila, Katja Eloranta, Marjut Pihlajoki, Mark Davenport, Markku Heikinheimo, Antti Kyronlahti, Mikko P. Pakarinen
Summary: This study investigates the utility of secretin receptor (SCTR) as a potential biomarker for predicting native liver survival and clearance of jaundice after portoenterostomy (PE) surgery in patients with biliary atresia (BA). The results show that higher expression of SCTR is associated with lower 5-year native liver survival and clearance of jaundice after PE. SCTR expression also correlates with liver fibrosis, ductular reaction, and markers of fibrosis and cholangiocytes. Therefore, SCTR may serve as a promising prognostic marker for PE outcomes and liver injury in BA.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Diana Medina-Felix, Francisco Vargas-Albores, Estefania Garibay-Valdez, Luis Rafael Martinez-Cordova, Marcel Martinez-Porchas
Summary: In this research, the effects of Nocardia infection on fish gastrointestinal microbiota were analyzed. It was found that the infection led to decreased survival rate, severe damage to the stomach microbiota, and a significant increase in Proteobacteria. A negative correlation network between Proteobacteria and other important phyla was observed. Therefore, Nocardia sp. is an emerging pathogen capable of inducing dysbiosis and causing significant mortalities.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Lele Wu, Wen Sun, Jiale Zhou, Yaolin Li, Jun Li, Zongcheng Song, Changbin Song, Shihong Xu, Xinlu Yue, Xian Li
Summary: The study finds that red light induces dichromatic skin pigmentation in turbot juveniles, with some individuals displaying black coloration and others displaying lighter skin. The upregulated gene expressions related to melanin synthesis and the involvement of the nervous system in spectral environment-driven color regulation are both crucial factors.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2024)