Article
Multidisciplinary Sciences
Rotimi Fasimoye, Wentao Dong, Raja S. Nirujogi, Eshaan S. Rawat, Miharu Iguchi, Kwamina Nyame, Toan K. Phung, Enrico Bagnoli, Alan R. Prescott, Dario R. Alessi, Monther Abu-Remaileh
Summary: The Golgi is a crucial organelle involved in protein and lipid biosynthesis, as well as sorting and secretion. Dysfunctional Golgi is associated with various diseases. This study presents a Golgi immunoprecipitation technique to isolate intact Golgi mini-stacks for analysis. The analysis pipeline reveals the molecular features of the human Golgi, including proteome, metabolome, and lipidome profiles. This comprehensive molecular map provides a powerful method to study the Golgi in health and disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Kam Sang Kwok, Yi Zuo, Soo Jin Choi, Gayatri J. Pahapale, Luo Gu, David H. Gracias
Summary: Lithographic nanopatterning techniques have been widely used in electronics and optics, but their application in nanobio interfaces is limited by cytotoxicity and 2D features. This article presents a biocompatible and cost-effective transfer process using nanoimprint lithography and alginate hydrogel to create flexible and degradable transfer layers. Biotransfer printing of the nanopattern arrays on live cells and animal brains demonstrates high pattern fidelity and cell viability. This method has great potential in advancing bionics, biosensing, and biohybrid tissue interfaces.
Article
Cell Biology
Kinga Dora Kovacs, Tamas Visnovitz, Tamas Gerecsei, Beatrix Peter, Sandor Kurunczi, Anna Koncz, Krisztina Nemeth, Dorina Lenzinger, Krisztina V. Vukman, Anna Balogh, Imola Rajmon, Peter Lorincz, Inna Szekacs, Edit I. Buzas, Robert Horvath
Summary: Extracellular vesicles (EVs) have gained significant attention in biomedicine in the past decade. This report describes the direct nanoinjection of EVs into single cells using robotic fluidic force microscopy (robotic FluidFM). The study demonstrates the feasibility of nanoinjecting EVs and EV-like particles into various cell lines, providing valuable insights into cellular responses to EVs.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Biochemistry & Molecular Biology
Nathan M. Livingston, Jiwoong Kwon, Oliver Valera, James A. Saba, Niladri K. Sinha, Pranav Reddy, Blake Nelson, Clara Wolfe, Taekjip Ha, Rachel Green, Jian Liu, Bin Wu
Summary: Stochasticity has been found to play a role in gene regulation, particularly in bursting transcription. However, the role of stochasticity in translation has not been fully explored due to limitations in imaging technology. This study developed techniques to track single mRNAs and their translation in live cells, revealing previously unknown dynamics of translation. The findings show that translation, like transcription, occurs in bursts of activity and inactivity, but with complex structures in the untranslated region affecting burst amplitudes. Bursting frequency can be controlled by specific sequences and trans-acting factors.
Article
Cell Biology
Sven Lyschik, Anna A. Lauer, Tanja Roth, Daniel Janitschke, Markus Hollander, Thorsten Will, Tobias Hartmann, Ron R. Kopito, Volkhard Helms, Marcus O. W. Grimm, Bianca Schrul
Summary: Cellular lipid metabolism is tightly regulated by PEX19, which targets proteins to peroxisomes and lipid droplets. PEX19 plays a crucial role in controlling neutral lipid storage and dynamics by sorting specific protein subsets to lipid droplets.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ioannis Tsirkas, Daniel Dovrat, Manikandan Thangaraj, Ineke Brouwer, Amit Cohen, Zohar Paleiov, Michael M. Meijler, Tineke Lenstra, Amir Aharoni
Summary: The coexistence of DNA replication and transcription during S-phase requires tight coordination to prevent conflicts. This study developed a live-cell imaging approach to monitor the real-time progression of replisomes and transcription dynamics during a transcription-replication encounter. The findings showed a wave of partial transcriptional repression ahead of the moving replication fork, and revealed the negative impact of conflicts on both processes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Weisong Zhao, Shiqun Zhao, Liuju Li, Xiaoshuai Huang, Shijia Xing, Yulin Zhang, Guohua Qiu, Zhenqian Han, Yingxu Shang, De-En Sun, Chunyan Shan, Runlong Wu, Lusheng Gu, Shuwen Zhang, Riwang Chen, Jian Xiao, Yanquan Mo, Jianyong Wang, Wei Ji, Xing Chen, Baoquan Ding, Yanmei Liu, Heng Mao, Bao-Liang Song, Jiubin Tan, Jian Liu, Haoyu Li, Liangyi Chen
Summary: Sparse structured illumination microscopy (Sparse-SIM) achieves nearly twofold resolution enhancement by utilizing sparse deconvolution algorithm, enabling the resolution of intricate biological structures such as small fusion pores, nuclear pores, and relative movements of inner and outer mitochondrial membranes.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Wanze Chen, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G. Gaebelein, Wouter Saelens, Vincent Gardeux, Amanda Klaeger, Riccardo Dainese, Magda Zachara, Tomaso Zambelli, Julia A. Vorholt, Bart Deplancke
Summary: Live-seq is a novel single-cell transcriptomic profiling approach that preserves cell viability during RNA extraction, allowing for the correlation analysis between a cell's ground-state transcriptome and its downstream molecular or phenotypic behavior. It accurately stratifies diverse cell types and states without major cellular perturbations, and can be used to map a cell's trajectory and evaluate gene effects on cell phenotypes.
Article
Biotechnology & Applied Microbiology
Chang Qiao, Di Li, Yong Liu, Siwei Zhang, Kan Liu, Chong Liu, Yuting Guo, Tao Jiang, Chuyu Fang, Nan Li, Yunmin Zeng, Kangmin He, Xueliang Zhu, Jennifer Lippincott-Schwartz, Qionghai Dai, Dong Li
Summary: In this study, a rationalized deep learning (rDL) method was developed for improving optical microscopy imaging by addressing artifacts and noise. By incorporating prior knowledge of illumination patterns, the rDL method effectively denoises raw images and enhances the super-resolution information. Moreover, the method can perform self-supervised training using the continuity of noisy data itself, achieving results comparable to supervised methods.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bei Liu, Orrin J. Stone, Michael Pablo, J. Cody Herron, Ana T. Nogueira, Onur Dagliyan, Jonathan B. Grimm, Luke D. Lavis, Timothy C. Elston, Klaus M. Hahn
Summary: The approach utilizes binder/tag to study the conformation of individual proteins during single particle tracking in living cells, allowing for the tracking of protein trajectory and conformation, and providing highly specific biosensors.
Article
Biochemical Research Methods
Hao-Yang Liu, Zhi-Gang Wang, Shu-Lin Liu, Dai-Wen Pang
Summary: Single-virus tracking (SVT) allows real-time monitoring of individual viruses, enabling the exploration of their interactions with cellular structures. Quantum dot-based SVT (QSVT) overcomes the limitations of conventional fluorescent tags, providing more accurate and detailed information about viral infection in live cells.
Article
Chemistry, Analytical
Kyle D. G. Saunders, Johanna von Gerichten, Holly-May Lewis, Priyanka Gupta, Matt Spick, Catia Costa, Eirini Velliou, Melanie J. Bailey
Summary: In this study, nanocapillary sampling combined with liquid chromatography-mass spectrometry was used for single-cell lipidomics. The method showed high sensitivity, allowing the tentative identification of around 260 lipids in a single cell. By analyzing the lipid profiles, chemotherapeutic drug-treated cancer cells were distinguished from control cells, and the relative abundance of LPC(0:0/16:0) was found to be significantly affected.
ANALYTICAL CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Mingsheng Zhu, Jie Zhuang, Zhe Li, Qiqi Liu, Rongping Zhao, Zhanxia Gao, Adam C. Midgley, Tianyi Qi, Jingwei Tian, Zhixuan Zhang, Deling Kong, Jie Tian, Xiyun Yan, Xinglu Huang
Summary: Using genetically tailored protein-based nanoprobes and taking advantage of image-segmentation-based machine learning (nano-ISML), a high-throughput assessment of vascular permeability of individual blood vessels in 32 different tumours is quantified. These insights are valuable in developing personalized anticancer nanomedicine therapeutics and strategies modulating vascular permeability to treat tumours.
NATURE NANOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Charlotte A. Cialek, Gabriel Galindo, Tatsuya Morisaki, Ning Zhao, Taiowa A. Montgomery, Timothy J. Stasevich
Summary: The authors developed live-cell biosensors to investigate the impact of Argonaute proteins on single-mRNA translation dynamics. They found that Argonaute association gradually silences translation and leads to the clustering and coalescence of mRNA with P-bodies, maintaining a translationally silent state.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Su Liang, Zeyu Wang, Luyu Qi, Chao Tang, Yiming Zhang, Qun Luo, Yayun Wu, Jinghe Yuan, Yao Zhao, Yanyan Zhang, Xiaohong Fang, Shijun Wang, Fuyi Wang
Summary: This study designed a fluorescent probe, ATTO565-WGN, which showed similar anti-proliferative activity to wogonin against human cancer cell lines and demonstrated mitochondrial localization through confocal fluorescence imaging. The conjugated ATTO565 fluorophore enabled STED fluorescence living cell imaging with ultrahigh spatial resolution, facilitating the investigation of wogonin-biological target interactions in living cells at mitochondria. This work provides novel insights into rational design of mitochondrion targeting fluorescence probes for ultrahigh resolution living cell imaging.
Article
Multidisciplinary Sciences
Di Yu, Yang Liu, Yiqiang Zhou, Victor Ruiz-Rodado, Mioara Larion, Guowang Xu, Chunzhang Yang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Review
Chemistry, Analytical
Artem Pliss, Paras N. Prasad
METHODS AND APPLICATIONS IN FLUORESCENCE
(2020)
Article
Nanoscience & Nanotechnology
Ting Zhou, Artem Pliss, Yu Chen, Andrey N. Kuzmin, Paras N. Prasad, Junle Qu
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE
(2020)
Article
Chemistry, Multidisciplinary
Julia C. Bulmahn, Gleb Tikhonowski, Anton A. Popov, Andrey Kuzmin, Sergey M. Klimentov, Andrei Kabashin, Paras N. Prasad
Article
Multidisciplinary Sciences
Adrian Lita, Artem Pliss, Andrey Kuzmin, Tomohiro Yamasaki, Lumin Zhang, Tyrone Dowdy, Christina Burks, Natalia de Val, Orieta Celiku, Victor Ruiz-Rodado, Elena-Raluca Nicoli, Michael Kruhlak, Thorkell Andresson, Sudipto Das, Chunzhang Yang, Rebecca Schmitt, Christel Herold-Mende, Mark R. Gilbert, Paras N. Prasad, Mioara Larion
Summary: This study reveals that IDH1(mut) results in an increase in monounsaturated fatty acids and their phospholipids in the endoplasmic reticulum, leading to Golgi and ER dilation. Inhibition of IDH1 mutation or SCD silencing restores ER and Golgi morphology, while D-2HG and oleic acid induces morphological defects in these organelles. Moreover, the overexpression of SCD induced by IDH1(mut) rearranges the distribution of lipids in the organelles of glioma cells, contributing to potential therapeutic implications.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Artem Pliss, Andrey N. Kuzmin, Adrian Lita, Rahul Kumar, Orieta Celiku, G. Ekin Atilla-Gokcumen, Omer Gokcumen, Dhyan Chandra, Mioara Larion, Paras N. Prasad
Summary: The Ramanomics platform enables molecular profiling of single organelles in live-cell environments using confocal Raman microspectrometry and biomolecular component analysis algorithms. Significant variations in organellar composition between different cell lines have been discovered, and Ramanomics has been proven effective in identifying diseased cells and revealing large-scale molecular transformations accompanying disease development in organelles.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Artem Pliss, Andrey N. Kuzmin, Paras N. Prasad, Supriya D. Mahajan
Summary: The SARS-CoV-2 virus can cause neurological conditions by invading the nervous system. The dysfunction of mitochondria in brain microglia cells is believed to play a role in the neuropathology of SARS-CoV-2. Using Raman microspectrometry, researchers found that infected microglia cells exhibited reduced mtDNA content and increased phospholipid saturation levels in mitochondria. These changes may be linked to increased synthesis of reactive oxygen species in the organelles.
ACS CHEMICAL NEUROSCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Faris Zaibaq, Tyrone Dowdy, Mioara Larion
Summary: Gliomas are highly aggressive cancer types that require novel drugs and targeted therapies. Recent research has identified a unique metabolic vulnerability in the sphingolipid pathways of gliomas that can weaken the characteristics of the cancer and enhance tumor cell death by altering the balance of sphingosine-1-phosphate (S1P) and ceramide.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemical Research Methods
Victor Ruiz-Rodado, Adrian Lita, Mioara Larion
Article
Optics
Soumik Siddhanta, Andrey N. Kuzmin, Artem Pliss, Alexander S. Baev, Sunil K. Khare, Pramit K. Chowdhury, Ashok K. Ganguli, Paras N. Prasad
Summary: This review provides a historical account of the evolution of Raman spectroscopy and discusses advancements that have allowed for the detection of single molecules and non-invasive analysis of organelles. It addresses the need for a consolidated overview of Raman spectroscopy's broad applications in biosensing, from fundamental biology to disease identification, drug screening, and quality control in food and agriculture. The review also highlights the convergence of Raman spectroscopy with bioanalysis, agriculture, and food quality control, and explores the potential of combining advanced spectroscopy with machine-learning algorithms to establish a new field known as Ramanomics. Future needs and opportunities are also discussed.
ADVANCES IN OPTICS AND PHOTONICS
(2023)
Review
Oncology
Matthew B. Watowich, Mark R. Gilbert, Mioara Larion
Summary: Despite advancements in understanding tumor biology, malignant gliomas in the central nervous system (CNS) remain incurable. T cell exhaustion, characterized by reduced effector function, sustained expression of inhibitory receptors, metabolic dysfunction, and epigenetic alterations, contributes to the failure of immunotherapy in CNS cancers. This article highlights recent progress in identifying the drivers of T cell exhaustion in glioma microenvironment and potential strategies to reverse this immune suppressive phenotype. Directly targeting immunosuppressive drivers in brain cancers would be a significant advancement in immunotherapy.
Article
Nanoscience & Nanotechnology
Micah Raab, Artiom Skripka, Julia Bulmahn, Artem Pliss, Andrey Kuzmin, Fiorenzo Vetrone, Paras Prasad
Summary: In this study, we synthesized multi-shell rare-earth doped nanoparticles and achieved independent control in NIR imaging and therapeutic action by using different excitation wavelengths. By generating downshifting emission upon 800 nm excitation and upconversion emission upon 980 nm irradiation, high-contrast NIR imaging in NIR-IIb of optical transparency and selective activation of the surface-bound photosensitizer RB for safer and more specific therapy were achieved.
ACS APPLIED BIO MATERIALS
(2022)