Article
Immunology
Danielle Rodrigues Cortez, Fabio Mitsuo Lima, Joao Luis Reis-Cunha, Daniella Castanheira Bartholomeu, Rolando Andre Rios Villacis, Silvia Regina Rogatto, Andre Guilherme Costa-Martins, Fernanda Sycko Marchiano, Rafaela Andrade do Carmo, Jose Franco da Silveira, Marjorie Mendes Marini
Summary: In this study, the genetic differences between two lineages of Chagas disease-causing parasite T. cruzi were analyzed using intraspecific array-based comparative genomic hybridization (aCGH). The results showed that clone D11 had more chromosomal gains and losses compared to the parental G strain. These genomic changes suggest a dynamic genome in clone D11 that responds to environmental stress by altering gene copy numbers and generating segmental aneuploidy.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Keiji Ogura, Yoshiko Ayabe, Chihiro Harada, Ignacia Braga Tanaka, Satoshi Tanaka, Jun-ichiro Komura
Summary: This study reported the transgenerational effects of chronic low dose-rate irradiation in mice, revealing an increase in de novo copy number variations in the offspring of irradiated male mice. However, no significant difference was found in the size of the de novo deletions between the irradiated and non-irradiated groups. Further analysis suggested a potential association between de novo copy-number variations and shorter life spans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Jill Jasmine Dalimot, Ilka Mc Cormick Smith, Jasmin Gerkrath, Sylvia Hartmann, Oliver A. Cornely, Soo Chan Lee, Joseph Heitman, Volker Rickerts
Summary: This study focused on improving the accuracy of mucormycosis diagnosis from tissue samples using fluorescence in situ hybridization (FISH) targeting specific regions of fungal ribosomal RNA (rRNA) of Mucorales. While the probe combination showed success in targeting Mucorales and enhancing diagnosis, autofluorescence and variations in physiological states of fungi and antifungal therapy may impact the FISH signal obtained. Further studies are needed to determine the value of FISH in diagnosing mucormycosis from different clinical samples.
Article
Biochemical Research Methods
Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gomez-Sjoberg
Summary: This paper introduces an open-source toolkit and framework that incorporates crowdsourced and expert annotations as a source of ground truth for in situ transcriptomics image analysis. Through exploring and demonstrating the use of crowdsourced annotations for validating spot-calling algorithms and tuning parameters, it confirms that consensus crowdsourced annotations can substitute expert-generated ground truth. Advancements in in situ methods deepen our understanding of spatial organization in biological processes within tissues.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Microbiology
Demosthenes P. Morales, Aaron J. Robinson, Andrew C. Pawlowski, Caitlyn Ark, Julia M. Kelliher, Pilar Junier, James H. Werner, Patrick S. G. Chain
Summary: This study evaluates the challenges in resolving bacterial-fungal interactions and proposes the use of fluorescence in situ hybridization (FISH) for microscopy imaging to obtain more conclusive evidence on the nature of specific relationships between bacteria and fungi.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Bowen Zhang, Taoran Tian, Dexuan Xiao, Shaojingya Gao, Xiaoxiao Cai, Yunfeng Lin
Summary: A DNA-enhanced HCR detection system (T-probe system) is introduced for the detection of cancer-related targets, demonstrating its versatility and efficiency by detecting miRNA-21 and nucleolin. The T-probe system shows high detection rate and rapid recognition of both membrane and intracellular cancer-related targets, and exhibits superior fluorescence for imaging tumor-related biomarkers in vitro and in vivo, indicating its great potential for clinical diagnosis and therapeutic applications.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Plant Sciences
Yahui Xuan, Sheng Wang, Siwei Li, Jianglian Yuan, Qiming Zhou, Ningjia He
Summary: This study used cGISH and self-GISH methods to investigate the chromosome constitution and genetic relationships of 40 mulberry accessions. Multiple homozygous and heterozygous signal patterns were discovered, and five mulberry sections and their genetic relationships were defined. These findings are important for guiding hybrid breeding of perennial crops like mulberry.
Article
Cell Biology
Lu Xiao, Joshua Labaer, Jia Guo
Summary: A high sensitivity and specificity multiplexed in situ RNA profiling approach was developed, allowing for successful analysis of multiple RNA species in various types of tissues through cycles of RNA staining, signal amplification, and probe stripping.
Article
Biochemistry & Molecular Biology
Igor N. Lebedev, Tatyana Karamysheva, Eugeny A. Elisaphenko, Alexey Makunin, Daria Zhigalina, Maria E. Lopatkina, Gleb Drozdov, Aleksander D. Cheremnykh, Natalia B. Torkhova, Gulnara N. Seitova, Stanislav A. Vasilyev, Anna A. Kashevarova, Ludmila P. Nazarenko, Nikolay B. Rubtsov
Summary: The case study presented a prenatal diagnosis of a foetus with mosaic sSMC(10) and identified a ring structure derived from chromosome 10 with specific regions involved. Despite the presence of a 9 Mb euchromatin region, the sSMC did not result in clinical manifestations and a healthy girl was born. The study suggests that the ring structure of sSMCs could influence their manifestations and should be considered in genetic counselling during prenatal diagnosis.
Article
Multidisciplinary Sciences
Gerrit G. Tamminga, Gijsbert J. Jansen, Marit Wiersma
Summary: This study evaluated a non-invasive fluorescence in situ hybridization (FISH) method for the detection of SARS-CoV-2 in saliva and found it to have high sensitivity and specificity, making it suitable for general population testing.
Article
Neurosciences
Elena Daoud, Kelsey Zhu, Bruce Mickey, Hussein Mohamed, Mandisa Wen, Michael Delorenzo, Ivy Tran, Jonathan Serrano, Kimmo J. Hatanpaa, Jack M. Raisanen, Matija Snuderl, Chunyu Cai
Summary: Chordoid meningioma is a morphological variant of meningioma with unique methylation profiles, copy number variations, and mutations in chromatin remodeling genes. The prognosis of chordoid meningioma is comparable to WHO grade 1 meningioma and better than WHO grade 2 meningioma.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Marine & Freshwater Biology
Zeyu Jia, Yijing Dong, Heng Xu, Fengping Wang
Summary: The study optimized the HCR-FISH protocol to address the issues of low signal intensity and false-positive signals, successfully identifying HCR initiator/amplifier pairs with high efficiency and specificity. Through the optimization of sample pretreatment methods, HCR-FISH protocol combinations, and image processing, false positive signals were reduced.
MARINE LIFE SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Irfan Akhtar, Fiona A. Stewart, Anna Haerle, Andrea Droste, Mathias Beller
Summary: The researchers optimized a FISH protocol to detect major bacteria genera in the Drosophila gut microbiome, aiming to investigate their spatial localization. This study contributes to answering questions about regionalization and establishment of the gut microbiome.
Article
Biochemistry & Molecular Biology
Soumya Sundar Mati, Sourav Chowdhury, Soumen Sarkar, Nanigopal Bera, Nilmoni Sarkar
Summary: In this study, a newly synthesized compound called ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) showed selectivity in binding to the minor groove A-T base pair of genomic DNAs. The compound demonstrated strong binding preference for A-T rich groove over other sequences. Spectroscopic experiments confirmed the binding strength, while computational modeling revealed the binding mechanism. PQN also exhibited low cytotoxicity and efficient intracellular localization, suggesting its potential as a lead compound for nucleic acid therapeutics.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Charleen Chu, Yuan Liu, Manish Verma, Kent Wang, P. Otero, Bill Chen, Rama Mallampalli
Article
Biochemistry & Molecular Biology
Manish Verma, Jianhui Zhu, Kent Z. Q. Wang, Charleen T. Chu
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Wan-Yang Sun, Vladimir A. Tyurin, Karolina Mikulska-Ruminska, Indira H. Shrivastava, Tamil S. Anthonymuthu, Yu-Jia Zhai, Ming-Hai Pan, Hai-Biao Gong, Dan-Hua Lu, Jie Sun, Wen-Jun Duan, Sergey Korolev, Andrey Y. Abramov, Plamena R. Angelova, Ian Miller, Ofer Beharier, Gao-Wei Mao, Haider H. Dar, Alexandr A. Kapralov, Andrew A. Amoscato, Teresa G. Hastings, Timothy J. Greenamyre, Charleen T. Chu, Yoel Sadovsky, Ivet Bahar, Hulya Bayir, Yulia Y. Tyurina, Rong-Rong He, Valerian E. Kagan
Summary: By hydrolyzing 15-HpETE-PE, iPLA(2)beta prevents ferroptosis, while its dysfunction increases cellular sensitivity to ferroptosis. Mutations in PLA2G6 gene may be implicated in the pathogenesis of Parkinson's disease.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Genetics & Heredity
Bharesh K. Chauhan, Anagha Medsinge, Hannah L. Scanga, Charleen T. Chu, Ken K. Nischal
Summary: This study investigated the causal mechanisms of congenital corneal opacities (CCO) by phenotyping, histopathology analysis, and assessment of transcriptomic changes. A novel mechanism and two key players contributing to CCO were identified based on the findings.
MOLECULAR GENETICS AND METABOLISM REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Daniel J. Klionsky, Giulia Petroni, Ravi K. Amaravadi, Eric H. Baehrecke, Andrea Ballabio, Patricia Boya, Jose Manuel Bravo-San Pedro, Ken Cadwell, Francesco Cecconi, Augustine M. K. Choi, Mary E. Choi, Charleen T. Chu, Patrice Codogno, Maria Isabel Colombo, Ana Maria Cuervo, Vojo Deretic, Ivan Dikic, Zvulun Elazar, Eeva-Liisa Eskelinen, Gian Maria Fimia, David A. Gewirtz, Douglas R. Green, Malene Hansen, Marja Jaattela, Terje Johansen, Gabor Juhasz, Vassiliki Karantza, Claudine Kraft, Guido Kroemer, Nicholas T. Ktistakis, Sharad Kumar, Carlos Lopez-Otin, Kay F. Macleod, Frank Madeo, Jennifer Martinez, Alicia Melendez, Noboru Mizushima, Christian Munz, Josef M. Penninger, Rushika M. Perera, Mauro Piacentini, Fulvio Reggiori, David C. Rubinsztein, Kevin M. Ryan, Junichi Sadoshima, Laura Santambrogio, Luca Scorrano, Hans-Uwe Simon, Anna Katharina Simon, Anne Simonsen, Alexandra Stolz, Nektarios Tavernarakis, Sharon A. Tooze, Tamotsu Yoshimori, Junying Yuan, Zhenyu Yue, Qing Zhong, Lorenzo Galluzzi, Federico Pietrocola
Summary: Autophagy is crucial for maintaining cellular and organismal homeostasis, and dysfunction in autophagy is implicated in the pathogenesis of major human disorders across various organ systems.
Review
Biochemistry & Molecular Biology
Britney N. Lizama, Charleen T. Chu
Summary: Autophagy is crucial for cells to remove damaged components and is increasingly studied for its role in various diseases. Research on autophagy and mitochondrial quality control is expanding, particularly in relation to conditions like cancer, immune diseases, and neurodegenerative diseases.
MOLECULAR ASPECTS OF MEDICINE
(2021)
Article
Ophthalmology
Parth R. Shah, Bharesh Chauhan, Charleen T. Chu, Julia Kofler, Ken K. Nischal
Summary: In this study, deep ocular phenotyping of Peters-plus syndrome was performed using anterior segment optical coherence tomography and ultrasound biomicroscopy. The most common ocular phenotype observed was an avascular paracentral ring opacity with relative central clearing. A different phenotype with a large vascularized corneal opacity was also identified.
Review
Neurosciences
Manish Verma, Britney N. Lizama, Charleen T. Chu
Summary: Glutamate is a commonly used neurotransmitter in the central nervous system of mammals, but excessive levels can lead to excitotoxicity and neuronal cell death. Excitatory synaptic dysregulation also contributes to neurodegeneration. Optimizing mitochondrial calcium flux can prevent excitatory mitochondrial toxicity and provide neuroprotection in various diseases.
TRANSLATIONAL NEURODEGENERATION
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Britney N. Lizama, Kent Z. Wang, Manish Verma, Jianhui Zhu, Abigail Skeel, Charleen T. Chu
Meeting Abstract
Biochemistry & Molecular Biology
Charleen T. Chu, Gabriella Fricklas, Aparna Nigam, Britney N. Lizama, Zachary P. Wills, Jon W. Johnson, P. Anthony Otero
Article
Neurosciences
P. Anthony Otero, Gabriella Fricklas, Aparna Nigam, Britney N. Lizama, Zachary P. Wills, Jon W. Johnson, Charleen T. Chu
Summary: Mutations in the PINK1 gene contribute to abnormal dendritic and spine structures, resulting in increased risk of cognitive and neuropsychiatric symptoms.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Pathology
Manish Verma, Lily Francis, Britney N. Lizama, Jason Callio, Gabriella Fricklas, Kent Z. Q. Wang, Brett A. Kaufman, Leonardo D'Aiuto, Donna B. Stolz, Simon C. Watkins, Vishwajit L. Nimgaonkar, Alejandro Soto-Gutierrez, Amy Goldstein, Charleen T. Chu
Summary: Mutations in the POLG gene lead to mitochondrial DNA depletion syndrome, with the brain being one of the most affected organs. Patient-derived iPSCs were used to investigate mechanisms and potential treatments for this condition.
AMERICAN JOURNAL OF PATHOLOGY
(2023)
Article
Genetics & Heredity
Elena Franco, Hannah L. Scanga, Soosan Jacob, Charleen T. Chu, Ken K. Nischal
Summary: 8q21.11 microdeletion syndrome is associated with congenital corneal staphyloma, likely due to a combination of anterior segment developmental anomalies and elevated intraocular pressure. Tectonic penetrating keratoplasty and strict control of intraocular pressure are necessary for management.
OPHTHALMIC GENETICS
(2023)
Meeting Abstract
Ophthalmology
An-Jey Su, Bing Li, Yong Wang, Charles R. Owens, Touka Banaee, Neil J. Khatter, Anna D. Lee, David Mathes, Evan Farkash, Charleen T. Chu, Christene Huang, Kia M. Washington
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Physiology
Charleen T. Chu
Summary: The brain is one of the most energetically demanding tissues in the human body, and mitochondrial pathology plays a significant role in chronic neurodegenerative diseases. Studies on familial neurodegeneration reveal a complex and nuanced relationship involving the entire mitochondrial life cycle.
CURRENT OPINION IN PHYSIOLOGY
(2022)
