Article
Chemistry, Analytical
Kinuko Koda, Sascha Keller, Ryosuke Kojima, Mako Kamiya, Yasuteru Urano
Summary: In this study, a new fluorescence probe, m-DiMeNAF488, was developed for measuring the acidic pH inside vesicles in living cells using fluorescence lifetime imaging microscopy (FLIM). The probe exhibits a pH-dependent equilibrium and distinct fluorescence lifetimes, allowing for the evaluation of pH changes in acidic vesicles. By using FLIM and m-DiMeNAF488, we were able to monitor the pH changes in phagosomes during phagocytosis.
ANALYTICAL CHEMISTRY
(2022)
Article
Environmental Sciences
Jun Li, Yinyin Zhou, Yanpin Qin, Jinkuan Wei, Pengyang Shigong, Haitao Ma, Yunqing Li, Xiangcheng Yuan, Liqiang Zhao, Hong Yan, Yuehuan Zhang, Ziniu Yu
Summary: The study found that juvenile symbiont-bearing giant clams show tolerance to moderate ocean acidification, but have sensitivity in their calcification physiology. This is reflected in reduced net calcification rate, as well as declines in symbiont photosynthetic yield and zooxanthellae density.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Food Science & Technology
Xin Zhang, Shuai Zhang, Dongyao Li, Na Zhang, Yu Wang, Miaoshu Wang, Hongtao Tian, Rajesh Jha, Chen Li
Summary: This study evaluated the correlation between candidate genes and acidity changes in yogurt and identified a biomarker for post-acidification. Through screening, niacin was found to be an effective food additive for inhibiting post-acidification. RNA-seq analysis revealed that niacin inhibits post-acidification by affecting protein synthesis and glycolysis.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Mei Zhang, Yu Zhen, Tiezhu Mi, Senjie Lin
Summary: Research has shown that rising atmospheric CO2 concentrations are causing ocean acidification with significant consequences for marine organisms. Studies on the temperate coastal marine diatom Skeletonema marinoi suggest that elevated CO2 levels can inhibit photosynthesis and growth, but induce cells to invest more in protein synthesis, energy metabolism, and antioxidative stress defense.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Marine & Freshwater Biology
Jiazhu Zhang, Qiongying Yang, Qianlou Liu, Shuqi Liu, Yue Zhu, Jiang Yao, Hong Wang, Wanchun Guan
Summary: This study investigated the transcriptional response of the toxic dinoflagellate Karenia mikimotoi to simulated ocean acidification (OA). It was found that under OA conditions, the physiological parameters and transcriptomes of the dinoflagellate were altered, with increased expression of antioxidant enzymes and key genes involved in energy metabolism, enhancing the ability to cope with low pH stress. Additionally, the study revealed that K. mikimotoi showed tolerance to ocean acidification.
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Editorial Material
Cell Biology
Meiqin Hu, Jingzhi Chen, Siyu Liu, Haoxing Xu
Summary: The TMEM175 gene encodes the LyPAP channel, which is essential for lysosomal proton leak currents and is most active during lysosomal hyper-acidification. Lack of TMEM175 leads to lysosomal hyper-acidification and impaired proteolytic degradation, while variants associated with susceptibility to Parkinson's disease cause a reduction in LyPAP currents and lysosomal hyper-acidification.
Article
Biology
Qing Wu, Li Ma, Lena Joesch-Cohen, Michael Schmidt, Ece D. Gamsiz Uzun, Eric M. Morrow
Summary: Through RNA-seq analysis, we identified the transcriptome signatures of Christianson syndrome (CS) caused by loss-of-function mutations in the SLC9A6 gene. Further research revealed critical modules associated with neurodevelopment and lysosome function.
Editorial Material
Biochemical Research Methods
John P. Chute, Joshua P. Sasine
Summary: Image-seq combines high-resolution microscopy with single-cell transcriptomics to spatially resolve and isolate viable bone marrow and leukemia cells, achieving a long-sought integration of single-cell molecular profiling and cellular spatial localization.
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Tal Ashuach, Mariano I. Gabitto, Rohan V. Koodli, Giuseppe-Antonio Saldi, Michael I. Jordan, Nir Yosef
Summary: Jointly profiling the transcriptome, chromatin accessibility, and other molecular properties of single cells can enhance the study of cellular diversity. MultiVI, a probabilistic model, allows the analysis of multiomic data and enhances single-modality datasets by creating a joint representation. It can be accessed at scvi-tools.org.
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Biochemistry & Molecular Biology
Sonia Garcia-Ruiz, Emil K. Gustavsson, David Zhang, Regina H. Reynolds, Zhongbo Chen, Aine Fairbrother-Browne, Ana Luisa Gil-Martinez, Juan A. Botia, Leonardo Collado-Torres, Mina Ryten
Summary: Dysregulation of RNA splicing is implicated in rare and complex diseases. We have developed IntroVerse, a comprehensive resource for exploring intron usage by providing a catalogue of annotated introns and novel junctions. This dataset, generated from extensive RNA sequencing analysis, offers insights into novel transcripts and assessment of splicing noise in introns.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Matthias Flotho, Jeremy Amand, Pascal Hirsch, Friederike Grandke, Tony Wyss-Coray, Andreas Keller, Fabian Kern
Summary: The molecular causes and mechanisms of neurodegenerative diseases are still not well understood. This study introduces ZEBRA, a large single-cell and single-nucleus RNA-seq database, which integrates gene expression and metadata from multiple studies to enhance our understanding of mammalian brain function during aging and disease.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Pearl P. Y. Lie, Dun-Sheng Yang, Philip Stavrides, Chris N. Goulbourne, Ping Zheng, Panaiyur S. Mohan, Anne M. Cataldo, Ralph A. Nixon
Summary: Research reveals that mature lysosomes are restricted from entering axons in neurons, while transport carriers derived from the TGN supply lysosomal components to axons. In axons, most LAMP1 vesicles are weakly acidic TCs that shuttle lysosomal components bidirectionally.
Editorial Material
Neurosciences
John J. Alam, Ralph A. Nixon
NEUROPSYCHOPHARMACOLOGY
(2022)
Article
Neurosciences
Ju-Hyun Lee, Dun-Sheng Yang, Chris N. Goulbourne, Eunju Im, Philip Stavrides, Anna Pensalfini, Han Chan, Cedric Bouchet-Marquis, Cynthia Bleiwas, Martin J. Berg, Chunfeng Huo, James Peddy, Monika Pawlik, Efrat Levy, Mala Rao, Mathias Staufenbiel, Ralph A. Nixon
Summary: This study reveals unique autophagy dysregulation within neurons in Alzheimer's disease mouse models, particularly deficient autolysosome acidification, leading to the accumulation of autophagic vacuoles and the formation of flower-like structures called "PANTHOS," which may contribute to the development of senile plaques in Alzheimer's disease.
NATURE NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Pearl P. Y. Lie, Lang Yoo, Chris N. Goulbourne, Martin J. Berg, Philip Stavrides, Chunfeng Huo, Ju-Hyun Lee, Ralph A. Nixon
Summary: This study reveals the dysfunction and mistrafficking of organelles in autophagy- and endosomal-lysosomal pathways associated with neurodegenerative diseases. The researchers found that degradative organelles in axons are selectively vulnerable to local calcium dysregulation, which is greatly influenced by the activation of TRPML1 channels. The study also identified a mechanism involving calcium-mediated JNK activation and DIC1B serine-80 phosphorylation that contributes to neuritic dystrophy.
Editorial Material
Cell Biology
Ju-Hyun Lee, Ralph A. Nixon
Summary: Genetic evidence has shown that lysosome dysfunction is linked to impaired autophagy-lysosomal pathway (ALP) flux in Alzheimer's disease (AD). This study discovered that autophagy dysfunction in mouse models of AD arises from early failure of autolysosome/lysosome acidification, which leads to downstream AD pathogenesis. These findings provide important insights into the sequence of events in plaque formation.
Article
Cell Biology
Mala Rao, Sandipkumar Darji, Philip H. Stavrides, Chris N. Goulbourne, Asok Kumar, Dun-Sheng Yang, Lang Yoo, James Peddy, Ju-Hyun Lee, Aidong Yuan, Ralph A. Nixon
Summary: This study reveals the important role of autophagy in the degradation of neurofilament proteins in neurons, which may regulate the size of axon cytoskeleton and the responses of the neurofilament cytoskeleton to injury and disease.
Article
Neurosciences
Aidong Yuan, Ralph A. Nixon
Summary: Neurofilament and tau proteins are involved in regulating stability and functions of the microtubule network in axons, axonal transport, and learning and memory. Their expression is regulated at the transcriptional and posttranscriptional levels, with RNA-binding proteins and microRNAs playing important roles in their regulation through the 3'-untranslated regions of their mRNA.
BRAIN RESEARCH BULLETIN
(2023)
Article
Multidisciplinary Sciences
Ying Jiang, John J. Alam, Stephen N. Gomperts, Paul Maruff, Afina W. Lemstra, Ursula A. Germann, Philip H. Stavrides, Sandipkumar Darji, Sandeep Malampati, James Peddy, Cynthia Bleiwas, Monika Pawlik, Anna Pensalfini, Dun-Sheng Yang, Shivakumar Subbanna, Balapal S. Basavarajappa, John F. Smiley, Amanda Gardner, Kelly Blackburn, Hui-May Chu, Niels D. Prins, Charlotte E. Teunissen, John E. Harrison, Philip Scheltens, Ralph A. Nixon
Summary: The study found that Rab5 is closely related to BFCN degeneration, and inhibiting Rab5 activity may be a method for treating related diseases. The use of neflamapimod reduced Rab5 activity, reversed endosomal pathology, and restored the number and morphology of BFCNs. The clinical trial in DLB patients showed that neflamapimod did not affect cognitive function, but there were improvements in functional mobility and dementia rating-scale, confirming its effect on BFCN function.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Neurosciences
John J. Alam, Ralph A. Nixon
MOLECULAR NEURODEGENERATION
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)
