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Santini T, Chen C, Zhu W, Liou JJ, Walker E, Venkatesh S, Farhat N, Sajewski A, Alkhateeb S, Saranathan M, Xia Z, Ibrahim TS. Hippocampal subfields and thalamic nuclei associations with clinical outcomes in multiple sclerosis: An ultrahigh field MRI study. Mult Scler Relat Disord 2024; 86:105520. [PMID: 38582026 DOI: 10.1016/j.msard.2024.105520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/14/2024] [Accepted: 02/25/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Previous studies have shown that thalamic and hippocampal neurodegeneration is associated with clinical decline in Multiple Sclerosis (MS). However, contributions of the specific thalamic nuclei and hippocampal subfields require further examination. OBJECTIVE Using 7 Tesla (7T) magnetic resonance imaging (MRI), we investigated the cross-sectional associations between functionally grouped thalamic nuclei and hippocampal subfields volumes and T1 relaxation times (T1-RT) and subsequent clinical outcomes in MS. METHODS High-resolution T1-weighted and T2-weighted images were acquired at 7T (n=31), preprocessed, and segmented using the Thalamus Optimized Multi Atlas Segmentation (THOMAS, for thalamic nuclei) and the Automatic Segmentation of Hippocampal Subfields (ASHS, for hippocampal subfields) packages. We calculated Pearson correlations between hippocampal subfields and thalamic nuclei volumes and T1-RT and subsequent multi-modal rater-determined and patient-reported clinical outcomes (∼2.5 years after imaging acquisition), correcting for confounders and multiple tests. RESULTS Smaller volume bilaterally in the anterior thalamus region correlated with worse performance in gait function, as measured by the Patient Determined Disease Steps (PDDS). Additionally, larger volume in most functional groups of thalamic nuclei correlated with better visual information processing and cognitive function, as measured by the Symbol Digit Modalities Test (SDMT). In bilateral medial and left posterior thalamic regions, there was an inverse association between volumes and T1-RT, potentially indicating higher tissue degeneration in these regions. We also observed marginal associations between the right hippocampal subfields (both volumes and T1-RT) and subsequent clinical outcomes, though they did not survive correction for multiple testing. CONCLUSION Ultrahigh field MRI identified markers of structural damage in the thalamic nuclei associated with subsequently worse clinical outcomes in individuals with MS. Longitudinal studies will enable better understanding of the role of microstructural integrity in these brain regions in influencing MS outcomes.
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Affiliation(s)
- Tales Santini
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Chenyi Chen
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Wen Zhu
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jr-Jiun Liou
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Elizabeth Walker
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Shruthi Venkatesh
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Nadim Farhat
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Andrea Sajewski
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Salem Alkhateeb
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States.
| | - Tamer S Ibrahim
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States; Department of Radiology, University of Pittsburgh, Pittsburgh, PA, United States.
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Marr EE, Isenberg BC, Wong JY. Effects of polydimethylsiloxane membrane surface treatments on human uterine smooth muscle cell strain response. Bioact Mater 2024; 32:415-426. [PMID: 37954466 PMCID: PMC10632608 DOI: 10.1016/j.bioactmat.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/14/2023] Open
Abstract
In the United States, 1 in 10 infants are born preterm. The majority of neonatal deaths and nearly a third of infant deaths are linked to preterm birth. Preterm birth is initiated when the quiescent state of the uterus ends prematurely, leading to contractions and parturition beginning as early as 32 weeks, though the origins are not well understood. To enable research and discovery of therapeutics with potential to better address preterm birth, the capability to study isolated cell processes of pregnant uterine tissue in vitro is needed. Our development of an in vitro model of the myometrium utilizing human uterine smooth muscle cells (uSMCs) responsible for contractions provides a methodology to examine cellular mechanisms of late-stage pregnancy potentially involved in preterm birth. We discuss culture of uSMCs on a flexible polydimethylsiloxane (PDMS) substrate functionalized with cationic poly-l-lysine (PLL), followed by extracellular matrix (ECM) protein coating. Previous work exploring uSMC behavior on PDMS substrates have utilized collagen-I coatings, however, we demonstrated the first exploration of human uSMC response to strain on fibronectin-coated flexible membranes, importantly reflecting the significant increase of fibronectin content found in the myometrial ECM during late-stage pregnancy. Using the model we developed, we conducted proof-of-concept studies to investigate the impact of substrate strain on uSMC cell morphology and gene expression. It was found that PLL and varied ECM protein coatings (collagen I, collagen III, and fibronectin) altered cell nuclei morphology and density on PDMS substrates. Additionally, varied strain rates applied to uSMC substrates significantly impacted uSMC gene expression of IL-6, a cytokine associated with instances of preterm labor. These results suggest that both surface and mechanical properties of in vitro systems impact primary human uSMC phenotype and offer uSMC culture methodologies that can be utilized to further the understanding of cellular pathways involved in the uterus under mechanical load.
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Affiliation(s)
- Elizabeth E. Marr
- Boston University, Division of Materials Science and Engineering, United States
- Charles Stark Draper Laboratory, Bioengineering Division, United States
| | - Brett C. Isenberg
- Charles Stark Draper Laboratory, Bioengineering Division, United States
| | - Joyce Y. Wong
- Boston University, Division of Materials Science and Engineering, United States
- Boston University, Department of Biomedical Engineering, United States
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Tam R, Harris TJC. Reshaping the Syncytial Drosophila Embryo with Cortical Actin Networks: Four Main Steps of Early Development. Results Probl Cell Differ 2024; 71:67-90. [PMID: 37996673 DOI: 10.1007/978-3-031-37936-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Drosophila development begins as a syncytium. The large size of the one-cell embryo makes it ideal for studying the structure, regulation, and effects of the cortical actin cytoskeleton. We review four main steps of early development that depend on the actin cortex. At each step, dynamic remodelling of the cortex has specific effects on nuclei within the syncytium. During axial expansion, a cortical actomyosin network assembles and disassembles with the cell cycle, generating cytoplasmic flows that evenly distribute nuclei along the ovoid cell. When nuclei move to the cell periphery, they seed Arp2/3-based actin caps which grow into an array of dome-like compartments that house the nuclei as they divide at the cell cortex. To separate germline nuclei from the soma, posterior germ plasm induces full cleavage of mono-nucleated primordial germ cells from the syncytium. Finally, zygotic gene expression triggers formation of the blastoderm epithelium via cellularization and simultaneous division of ~6000 mono-nucleated cells from a single internal yolk cell. During these steps, the cortex is regulated in space and time, gains domain and sub-domain structure, and undergoes mesoscale interactions that lay a structural foundation of animal development.
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Affiliation(s)
- Rebecca Tam
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Tony J C Harris
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada.
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Saleem KS, Avram AV, Yen CCC, Magdoom KN, Schram V, Basser PJ. Multimodal anatomical mapping of subcortical regions in marmoset monkeys using high-resolution MRI and matched histology with multiple stains. Neuroimage 2023; 281:120311. [PMID: 37634884 DOI: 10.1016/j.neuroimage.2023.120311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023] Open
Abstract
Subcortical nuclei and other deep brain structures play essential roles in regulating the central and peripheral nervous systems. However, many of these nuclei and their subregions are challenging to identify and delineate in conventional MRI due to their small size, hidden location, and often subtle contrasts compared to neighboring regions. To address these limitations, we scanned the whole brain of the marmoset monkeys in ex vivo using a clinically feasible diffusion MRI method, called the mean apparent propagator (MAP)-MRI, along with T2W and MTR (T1-like contrast) images acquired at 7 Tesla. Additionally, we registered these multimodal MRI volumes to the high-resolution images of matched whole-brain histology sections with seven different stains obtained from the same brain specimens. At high spatial resolution, the microstructural parameters and fiber orientation distribution functions derived with MAP-MRI can distinguish the subregions of many subcortical and deep brain structures, including fiber tracts of different sizes and orientations. The good correlation with multiple but distinct histological stains from the same brain serves as a thorough validation of the structures identified with MAP-MRI and other MRI parameters. Moreover, the anatomical details of deep brain structures found in the volumes of MAP-MRI parameters are not visible in conventional T1W or T2W images. The high-resolution mapping using novel MRI contrasts, combined and correlated with histology, can elucidate structures that were previously invisible radiologically. Thus, this multimodal approach offers a roadmap toward identifying salient brain areas in vivo in future neuroradiological studies. It also provides a useful anatomical standard reference for the region definition of subcortical targets and the generation of a 3D digital template atlas for the marmoset brain research (Saleem et al., 2023). Additionally, we conducted a cross-species comparison between marmoset and macaque monkeys using results from our previous studies (Saleem et al., 2021). We found that the two species had distinct patterns of iron distribution in subregions of the basal ganglia, red nucleus, and deep cerebellar nuclei, confirmed with T2W MRI and histology.
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Affiliation(s)
- Kadharbatcha S Saleem
- Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, United States; Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817, United States.
| | - Alexandru V Avram
- Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, United States; Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817, United States
| | - Cecil Chern-Chyi Yen
- National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, United States
| | - Kulam Najmudeen Magdoom
- Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, United States; Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817, United States
| | - Vincent Schram
- Microscopy and Imaging Core (MIC), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, United States
| | - Peter J Basser
- Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, United States
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Goyal P, Malviya R. Advances in nuclei targeted delivery of nanoparticles for the management of cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188881. [PMID: 36965678 DOI: 10.1016/j.bbcan.2023.188881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/16/2023] [Accepted: 03/21/2023] [Indexed: 03/27/2023]
Abstract
A carrier is inserted into the appropriate organelles (nucleus) in successful medication transport, crucial to achieving very effective illness treatment. Cell-membrane targeting is the major focus of using nuclei to localize delivery. It has been demonstrated that high quantities of anticancer drugs can be injected directly into the nuclei of cancer cells, causing the cancer cells to die and increasing the effectiveness of chemotherapy. There are several effective ways to functionalize Nanoparticles (NPs), including changing their chemical makeup or attaching functional groups to their surface to increase their ability to target organelles. To cause tumor cells to apoptosis, released medicines must engage with molecular targets on particular organelles when their concentration is high enough. Targeted medication delivery studies will increasingly focus on organelle-specific delivery.
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Affiliation(s)
- Priyanshi Goyal
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India.
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Admire L, Carson M, Crawford K, Nguyen E, Daniels T. Hair root staining with Hematoxylin: Increasing the rate of obtaining DNA profiles in forensic casework. Forensic Sci Int 2023; 343:111544. [PMID: 36592528 DOI: 10.1016/j.forsciint.2022.111544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/07/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Hair evidence collected during a forensic investigation has the potential to provide valuable sourcing information through DNA analysis of its root. Over time, hair examiners at the North Carolina State Crime Laboratory observed hair roots being sent for DNA analysis were not yielding profiles as expected. Recent advancements in the Forensic Biology Section's detection limits prompted research into whether changes to the current root removal protocol could increase the likelihood of developing a DNA profile from a hair root. An internal validation was completed for the method of Hematoxylin staining to screen telogen roots for DNA analysis. Over 900 head hairs from approximately 15 living donors were examined for telogen roots. Those roots were stained using Hematoxylin and examined for nuclei. The roots were separated into groups based on nuclei present: Group I (1-10 nuclei), Group II (11-20 nuclei), Group III (21-30 nuclei), Group IV (31-40 nuclei), and Group V (41 or greater nuclei). A set of 64 roots, including a Negative Control (0 nuclei) and a Positive Control (anagen or catagen roots), were sent for quantitative DNA analysis. The data showed a clear separation between Groups I and II, where 36% of Group I verses 80% of Group II passed the quantification cutoff. All samples in the Negative Control, Group I, and the Positive Control were then amplified along with a representative sample in Groups II through V. After amplification, the delineation between Groups I and II maintained with 27% of Group I verses 89% of Group II obtaining DNA profiles. As a result, the nuclei required to obtain a potential DNA profile at our laboratory is eleven or more. Prior to Hematoxylin, anagen, catagen, or telogen roots with follicular tissue were sent for DNA analysis, resulting in 32% of roots yielding DNA results. Following implementation of Hematoxylin into casework in March 2019, the success rate has more than doubled to 69%, illustrating the utility of Hematoxylin root staining in improving casework efficiency. Through this methodology, only roots with the best potential to develop a DNA profile are sent for testing, thereby decreasing DNA caseload, cost, and time of analysis. In fact, Hematoxylin staining has resulted in a 14% reduction in the number of hair roots forwarded for DNA analysis, meaning hairs not meeting nuclear threshold are preserved for future examinations.
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Affiliation(s)
- Lindsey Admire
- North Carolina State Crime Laboratory, Raleigh, NC, USA.
| | | | | | - Evie Nguyen
- North Carolina State Crime Laboratory, Raleigh, NC, USA
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7
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Xin X, Du F, Jiao Y. Plant Nuclei Isolation for Single-Nucleus RNA Sequencing. Methods Mol Biol 2023; 2686:307-311. [PMID: 37540366 DOI: 10.1007/978-1-0716-3299-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Transcriptome profiling has been significantly hampered by the heterogeneity among individual cells within a tissue or an organ. Recent advances in single cell transcriptome profiling have significantly advanced our understanding of the transcriptome. However, plant single-cell RNA sequencing (scRNA-seq) relies on the isolation of protoplasts, which is not only impossible for many cell types but also induces acute wounding responses. To solve these problems, single-nucleus RNA sequencing (snRNA-seq) has been applied to plant research, in which nuclei are isolated and subject to encapsulation and profiling. Compared with scRNA-seq, snRNA-seq can be applied to a wider range of tissue types and plant species. Nevertheless, fewer transcripts can be obtained from each nucleus than each protoplast. In this chapter, we describe a detailed and general protocol to prepare nuclei from plant tissues that are ready for subsequent library construction and high-throughput sequencing.
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Affiliation(s)
- Xu Xin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, China.
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8
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Berendzen KW, Grefen C, Sakamoto T, Slane D. Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry. Methods Mol Biol 2023; 2698:57-73. [PMID: 37682469 DOI: 10.1007/978-1-0716-3354-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. Additionally, leveraging next-generation sequencing (NGS) platforms efforts have been undertaken to evaluate the effects of chromatin accessibility, histone modifications, or even transcription factor binding sites. We have shown that Fluorescence-Activated Nuclear Sorting (FANS) is an effective means to characterize the transcriptomes of nuclei from different tissues. In light of our own technical and experimental developments, we extend this effort to combine FACS/FANS with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) for profiling individual cell types according to their chromatin and transcriptional states.
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Affiliation(s)
- Kenneth W Berendzen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Christopher Grefen
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Bochum, Germany
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Daniel Slane
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan.
- The University of Tokyo, Graduate School of Frontier Sciences, Department of Integrated Biosciences, Laboratory of Integrated Biology, Chiba, Japan.
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9
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Šimková H, Tulpová Z, Cápal P. Flow Sorting-Assisted Optical Mapping. Methods Mol Biol 2023; 2672:465-483. [PMID: 37335494 DOI: 10.1007/978-1-0716-3226-0_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Optical mapping-a technique that visualizes short sequence motives along DNA molecules of hundred kilobases to megabase in size-has found an important place in genome research. It is widely used to facilitate genome sequence assemblies and analyses of genome structural variations. Application of the technique is conditional on availability of highly pure ultra-long high-molecular-weight DNA (uHMW DNA), which is challenging to achieve in plants due to the presence of the cell wall, chloroplasts, and secondary metabolites, just as a high content of polysaccharides and DNA nucleases in some species. These obstacles can be overcome by employment of flow cytometry, enabling a fast and highly efficient purification of cell nuclei or metaphase chromosomes, which are afterward embedded in agarose plugs and used to isolate the uHMW DNA in situ. Here, we provide a detailed protocol for the flow sorting-assisted uHMW DNA preparation that has been successfully used to construct whole-genome as well as chromosomal optical maps for 20 plant species from several plant families.
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Affiliation(s)
- Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic.
| | - Zuzana Tulpová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
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10
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Kaseva T, Omidali B, Hippeläinen E, Mäkelä T, Wilppu U, Sofiev A, Merivaara A, Yliperttula M, Savolainen S, Salli E. Marker-controlled watershed with deep edge emphasis and optimized H-minima transform for automatic segmentation of densely cultivated 3D cell nuclei. BMC Bioinformatics 2022; 23:289. [PMID: 35864453 PMCID: PMC9306214 DOI: 10.1186/s12859-022-04827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The segmentation of 3D cell nuclei is essential in many tasks, such as targeted molecular radiotherapies (MRT) for metastatic tumours, toxicity screening, and the observation of proliferating cells. In recent years, one popular method for automatic segmentation of nuclei has been deep learning enhanced marker-controlled watershed transform. In this method, convolutional neural networks (CNNs) have been used to create nuclei masks and markers, and the watershed algorithm for the instance segmentation. We studied whether this method could be improved for the segmentation of densely cultivated 3D nuclei via developing multiple system configurations in which we studied the effect of edge emphasizing CNNs, and optimized H-minima transform for mask and marker generation, respectively. RESULTS The dataset used for training and evaluation consisted of twelve in vitro cultivated densely packed 3D human carcinoma cell spheroids imaged using a confocal microscope. With this dataset, the evaluation was performed using a cross-validation scheme. In addition, four independent datasets were used for evaluation. The datasets were resampled near isotropic for our experiments. The baseline deep learning enhanced marker-controlled watershed obtained an average of 0.69 Panoptic Quality (PQ) and 0.66 Aggregated Jaccard Index (AJI) over the twelve spheroids. Using a system configuration, which was otherwise the same but used 3D-based edge emphasizing CNNs and optimized H-minima transform, the scores increased to 0.76 and 0.77, respectively. When using the independent datasets for evaluation, the best performing system configuration was shown to outperform or equal the baseline and a set of well-known cell segmentation approaches. CONCLUSIONS The use of edge emphasizing U-Nets and optimized H-minima transform can improve the marker-controlled watershed transform for segmentation of densely cultivated 3D cell nuclei. A novel dataset of twelve spheroids was introduced to the public.
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Affiliation(s)
- Tuomas Kaseva
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital and University of Helsinki, P.O. Box 340, FI-00290, Helsinki, Finland
| | - Bahareh Omidali
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland
| | - Eero Hippeläinen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland.,HUS Medical Imaging Centre, Clinical Physiology and Nuclear Medicine, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Teemu Mäkelä
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital and University of Helsinki, P.O. Box 340, FI-00290, Helsinki, Finland.,Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland
| | - Ulla Wilppu
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital and University of Helsinki, P.O. Box 340, FI-00290, Helsinki, Finland
| | - Alexey Sofiev
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital and University of Helsinki, P.O. Box 340, FI-00290, Helsinki, Finland.,Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland
| | - Arto Merivaara
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, Helsinki, Finland
| | - Marjo Yliperttula
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, Helsinki, Finland
| | - Sauli Savolainen
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital and University of Helsinki, P.O. Box 340, FI-00290, Helsinki, Finland.,Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland
| | - Eero Salli
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital and University of Helsinki, P.O. Box 340, FI-00290, Helsinki, Finland.
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Saleem KS, Avram AV, Glen D, Yen CC, Ye FQ, Komlosh M, Basser PJ. High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology. Neuroimage 2021; 245:118759. [PMID: 34838750 DOI: 10.1016/j.neuroimage.2021.118759] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022] Open
Abstract
Subcortical nuclei and other deep brain structures are known to play an important role in the regulation of the central and peripheral nervous systems. It can be difficult to identify and delineate many of these nuclei and their finer subdivisions in conventional MRI due to their small size, buried location, and often subtle contrast compared to neighboring tissue. To address this problem, we applied a multi-modal approach in ex vivo non-human primate (NHP) brain that includes high-resolution mean apparent propagator (MAP)-MRI and five different histological stains imaged with high-resolution microscopy in the brain of the same subject. By registering these high-dimensional MRI data to high-resolution histology data, we can map the location, boundaries, subdivisions, and micro-architectural features of subcortical gray matter regions in the macaque monkey brain. At high spatial resolution, diffusion MRI in general, and MAP-MRI in particular, can distinguish a large number of deep brain structures, including the larger and smaller white matter fiber tracts as well as architectonic features within various nuclei. Correlation with histology from the same brain enables a thorough validation of the structures identified with MAP-MRI. Moreover, anatomical details that are evident in images of MAP-MRI parameters are not visible in conventional T1-weighted images. We also derived subcortical template "SC21" from segmented MRI slices in three-dimensions and registered this volume to a previously published anatomical template with cortical parcellation (Reveley et al., 2017; Saleem and Logothetis, 2012), thereby integrating the 3D segmentation of both cortical and subcortical regions into the same volume. This newly updated three-dimensional D99 digital brain atlas (V2.0) is intended for use as a reference standard for macaque neuroanatomical, functional, and connectional imaging studies, involving both cortical and subcortical targets. The SC21 and D99 digital templates are available as volumes and surfaces in standard NIFTI and GIFTI formats.
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12
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Ahmadli U, Sandmann M, Fuchs J, Lermontova I. Immunolabeling of Nuclei/Chromosomes in Arabidopsis thaliana. Methods Mol Biol 2022; 2382:19-28. [PMID: 34705231 DOI: 10.1007/978-1-0716-1744-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The cell cycle is a complex sequence of events by which cells grow and divide mitotically or meiotically. Mitosis results in the generation of two identical daughter cells, while meiosis generates gametes as a prerequisite for sexual reproduction. To study the localization and dynamics of proteins involved in the regulation and proceeding of the cell cycle, life cell imaging of proteins fused to fluorescent tags can be performed. However, in some cases this approach cannot be applied, e.g., due to low fluorescence intensity, fast bleaching, or degradation of recombinant proteins by the proteasome pathway. Instead, immunolabeling with protein-specific antibodies offers a useful approach for the analysis of intact cells. Alternatively, immunolabeling can also be applied to isolated and/or flow-sorted nuclei of particular cell cycle stages (G1, S, and G2) or of different endopolyploidy levels. The following chapter will detail indirect immunolabeling protocols to analyze the subcellular localization and distribution of cell cycle-specific proteins in Arabidopsis thaliana.
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Sandry J, Dobryakova E. Global hippocampal and selective thalamic nuclei atrophy differentiate chronic TBI from Non-TBI. Cortex 2021; 145:37-56. [PMID: 34689031 DOI: 10.1016/j.cortex.2021.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/04/2021] [Accepted: 08/12/2021] [Indexed: 12/27/2022]
Abstract
Traumatic brain injury (TBI) may increase susceptibility to neurodegenerative diseases later in life. One neurobiological parallel between chronic TBI and neurodegeneration may be accelerated aging and the nature of atrophy across subcortical gray matter structures. The main aim of the present investigation is to evaluate and rank the degree that subcortical gray matter atrophy differentiates chronic moderate-severe TBI from non-TBI participants by evaluating morphometric differences between groups. Forty individuals with moderate-severe chronic TBI (9.23 yrs from injury) and 33 healthy controls (HC) underwent high resolution 3D T1-weighted structural magnetic resonance imaging. Whole brain volume was classified into white matter, cortical and subcortical gray matter structures with hippocampi and thalami further segmented into subfields and nuclei, respectively. Extensive atrophy was observed across nearly all brain regions for chronic TBI participants. A series of multivariate logistic regression models identified subcortical gray matter structures of the hippocampus and thalamus as the most sensitive to differentiating chronic TBI from non-TBI participants (McFadden R2 = .36, p < .001). Further analyses revealed the pattern of hippocampal atrophy to be global, occurring across nearly all subfields. The pattern of thalamic atrophy appeared to be much more selective and non-uniform, with largest between-group differences evident for nuclei bordering the ventricles. Subcortical gray matter was negatively correlated with time since injury (r = -.31, p = .054), while white matter and cortical gray matter were not. Cognitive ability was lower in the chronic TBI group (Cohen's d = .97, p = .003) and correlated with subcortical structures including the pallidum (r2 = .23, p = .038), thalamus (r2 = .36, p = .007) and ventral diencephalon (r2 = .23, p = .036). These data may support an accelerated aging hypothesis in chronic moderate-severe TBI that coincides with a similar neuropathological profile found in neurodegenerative diseases.
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Affiliation(s)
- Joshua Sandry
- Psychology Department, Montclair State University, Montclair, NJ, USA.
| | - Ekaterina Dobryakova
- Center for Traumatic Brain Injury Research, Kessler Foundation, East Hanover, NJ, USA; Department of Physical Medicine and Rehabilitation, Rutgers-New Jersey Medical School Newark, NJ, USA
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Pérez-González O, Gomez-Flores R, Tamez-Guerra P. Mycelial compatibility, anastomosis, and nucleus numbers of eight Mexican Hirsutella citriformis strains isolated from Diaphorina citri. PeerJ 2021; 9:e11080. [PMID: 33976961 PMCID: PMC8061572 DOI: 10.7717/peerj.11080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background Among entomopathogenic fungi, H. citriformis has been recognized as potential biocontrol agent against the Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae). Nevertheless, this fungus is poorly characterized. Previous molecular studies have shown high sequence similarities among strains, but significant differences in Diaphorina citri virulence. Objective The aim of the present study was to determine mycelial compatibility and anastomosis, and nucleus numbers in mycelium and conidia of eight H. citriformis strains isolated from mycosed D. citri adults collected from several Mexican states. Methods Mycelial compatibility and anastomosis evaluation was performed after pairing strains, leading to 36 confrontations, and cultured in chlorate minimum medium to obtain mutants for vegetative compatibility group. Results Hypha or conidia nuclei were visualized with safranin-O and 3% KOH, and 0.05% trypan blue–lactophenol solution. H. citriformis strains showed compatibly and anastomosis events after confrontation. In addition, they showed one nucleus per conidium and mycelium section. It was not possible to obtain H. citriformis nit mutants from the chlorate concentrations tested. Conclusions To date, this is the first report demonstrating mycelial compatibility, anastomosis occurrence, and hyphae and conidia nuclei number among H. citriformis strains.
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Affiliation(s)
- Orquídea Pérez-González
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Ricardo Gomez-Flores
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Patricia Tamez-Guerra
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo Leon, Mexico
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Slane D, Berendzen KW, Witthöft J, Jürgens G. Transcriptomic Profiling of the Arabidopsis Embryonic Epidermis Using FANS in Combination with RNAseq. Methods Mol Biol 2021; 2122:151-164. [PMID: 31975302 DOI: 10.1007/978-1-0716-0342-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The fundamental mechanisms of cell identity and tissue establishment are important already from the very beginning of a plant's life and reiterate later during development. In order to unravel and understand the underlying mechanisms to generate differences that in turn lead to cell or tissue types, plant cells have to be separated and their transcriptional setup analyzed. We have previously demonstrated that fluorescence-activated nuclear sorting (FANS) is a powerful tool to generate nuclear transcriptomic profiles of the most inaccessible embryonic tissues. In this protocol, we extend this effort to combine FANS with next generation RNA sequencing (RNA-seq) to achieve early embryonic transcriptomes of Arabidopsis epidermis precursor tissue (protoderm) and the inner tissue counterpart.
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Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kenneth W Berendzen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Janika Witthöft
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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Hoque IT, Ibtehaz N, Chakravarty S, Rahman MS, Rahman MS. A contour property based approach to segment nuclei in cervical cytology images. BMC Med Imaging 2021; 21:15. [PMID: 33509110 PMCID: PMC7841885 DOI: 10.1186/s12880-020-00533-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/06/2020] [Indexed: 11/14/2022] Open
Abstract
Background Segmentation of nuclei in cervical cytology pap smear images is a crucial stage in automated cervical cancer screening. The task itself is challenging due to the presence of cervical cells with spurious edges, overlapping cells, neutrophils, and artifacts. Methods After the initial preprocessing steps of adaptive thresholding, in our approach, the image passes through a convolution filter to filter out some noise. Then, contours from the resultant image are filtered by their distinctive contour properties followed by a nucleus size recovery procedure based on contour average intensity value. Results We evaluate our method on a public (benchmark) dataset collected from ISBI and also a private real dataset. The results show that our algorithm outperforms other state-of-the-art methods in nucleus segmentation on the ISBI dataset with a precision of 0.978 and recall of 0.933. A promising precision of 0.770 and a formidable recall of 0.886 on the private real dataset indicate that our algorithm can effectively detect and segment nuclei on real cervical cytology images. Tuning various parameters, the precision could be increased to as high as 0.949 with an acceptable decrease of recall to 0.759. Our method also managed an Aggregated Jaccard Index of 0.681 outperforming other state-of-the-art methods on the real dataset. Conclusion We have proposed a contour property-based approach for segmentation of nuclei. Our algorithm has several tunable parameters and is flexible enough to adapt to real practical scenarios and requirements.
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Affiliation(s)
- Iram Tazim Hoque
- Department of CSE, BUET, ECE Building, West Palashi, Dhaka, Bangladesh
| | - Nabil Ibtehaz
- Department of CSE, BUET, ECE Building, West Palashi, Dhaka, Bangladesh
| | - Saumitra Chakravarty
- Department of Pathology, Bangabandhu Sheikh Mujib Medical University, Shahabag, Dhaka, Bangladesh
| | - M Saifur Rahman
- Department of CSE, BUET, ECE Building, West Palashi, Dhaka, Bangladesh
| | - M Sohel Rahman
- Department of CSE, BUET, ECE Building, West Palashi, Dhaka, Bangladesh.
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Dudás B. Anatomy and cytoarchitectonics of the human hypothalamus. Handb Clin Neurol 2021; 179:45-66. [PMID: 34225981 DOI: 10.1016/b978-0-12-819975-6.00001-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Due to the complexity of hypothalamic functions, the organization of the hypothalamus is extremely intricate. This relatively small brain area contains several nuclei, most of them are ill-defined regions without distinct boundaries; these nuclei are often connected with each other and other distant brain regions with similarly indistinct pathways. These hypothalamic centers control numerous key physiological functions including reproduction, growth, food intake, circadian rhythm, behavior, and autonomic balance via neural and endocrine signals. To understand the morphology of the hypothalamus is therefore extremely important, though it remains a stupendous task due to the complex organization of neuronal networks formed by the various neurotransmitter and neuromodulator systems.
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Affiliation(s)
- Bertalan Dudás
- Neuroendocrine Organization Laboratory, Lake Erie College of Osteopathic Medicine, Erie, PA, United States; Department of Anatomy, Histology and Embryology, University of Szeged, Szeged, Hungary.
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Abstract
Lipidomics approaches provide quantitative characterization of hundreds of lipid species from biological samples. Recent studies highlight the value of these methods in studying circadian biology, and their potential goes far beyond studying lipid metabolism per se. For example, lipidomics analyses of subcellular compartments can be used to determine daily rhythmicity of different organelles and their intracellular dynamics. In this chapter we describe in detail the procedure for around the clock shotgun lipidomics, from sample preparation to bioinformatics analyses. Sample preparation includes biochemical fractionation of nuclei and mitochondria from mouse liver harvested throughout the day. Lipid content is determined and quantified, in unbiased manner and with wide coverage, using multidimensional mass spectrometry shotgun lipidomics (MDMS-SL). Circadian parameters are then determined with nonparametric statistical tests. Overall, the approach described herein is applicable for various animal models, tissues, and organelles, and is expected to yield new insight on various aspects of circadian biology and lipid metabolism.
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Affiliation(s)
- Rona Aviram
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Abstract
DNA damage is one of the most impactful events in living organisms, leading to DNA sequence changes (mutation) and disruption of biological processes. A study has identified a protein called Damage Suppressor Protein (Dsup) in the tardigrade Ramazzotius varieornatus that has shown to reduce the effects of radiation damage in human cell cultures (Hashimoto in Nature Communications 7:12808, 2016). We have generated tobacco plants that express the codon-optimized tardigrade Dsup gene and examined their responses when treated with mutagenic chemicals, ultraviolet (UV) and ionizing radiations. Our studies showed that compared to the control plants, the Dsup-expressing plants grew better in the medium containing mutagenic ethylmethane sulfonate (EMS). RT-qPCR detected distinct expression patterns of endogenous genes involved in DNA damage response and repair in the Dsup plants in response to EMS, bleomycin, UV-C and X-ray radiations. Comet assays revealed that the nuclei from the Dsup plants appeared more protected from UV and X-ray damages than the control plants. Overall, our studies demonstrated that Dsup gene expression enhanced tolerance of plants to genomutagenic stress. We suggest the feasibility of exploring genetic resources from extremotolerant species such as tardigrades to impart plants with tolerance to stressful environments for future climate changes and human space endeavors.
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Affiliation(s)
- Justin Kirke
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Xiao-Lu Jin
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Xing-Hai Zhang
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA.
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Abstract
Cyclic GMP-AMP (cGAMP) synthase (cGAS) is a cytosolic DNA sensor and innate immune response initiator. Binding with exogenous or endogenous nucleic acids, cGAS activates its downstream adaptor, stimulator of interferon genes (STING). STING then triggers protective immune to enable the elimination of the pathogens and the clearance of cancerous cells. Apparently, aberrantly activated by self-DNA, cGAS/STING pathway is threatening to cause autoimmune and inflammatory diseases. The effects of cGAS/STING in defenses against infection and autoimmune diseases have been well studied, still it is worthwhile to discuss the roles of cGAS/STING pathway beyond the “classical” realm of innate immunity. Recent studies have revealed its involvement in non-canonical inflammasome formation, calcium hemostasis regulation, endoplasmic reticulum (ER) stress response, perception of leaking mitochondrial DNA (mtDNA), autophagy induction, cellular senescence and senescence-associated secretory phenotype (SASP) production, providing an exciting area for future exploration. Previous studies generally focused on the function of cGAS/STING pathway in cytoplasm and immune response. In this review, we summarize the latest research of this pathway on the regulation of other physiological process and STING independent reactions to DNA in micronuclei and nuclei. Together, these studies provide a new perspective of cGAS/STING pathway in human diseases.
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Affiliation(s)
- Menghui Gao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Yuchen He
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Haosheng Tang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Xiangyu Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078, China. .,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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Xue L, Sun J, Zhu J, Ding Y, Chen S, Ding M, Pei H. The patterns of exercise-induced β-endorphin expression in the central nervous system of rats. Neuropeptides 2020; 82:102048. [PMID: 32446530 DOI: 10.1016/j.npep.2020.102048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
Abstract
Exercise at different intensities is able to induce different physical and psychological statuses of the subjects. The β-endorphin (β-EP) in central nervous system is thought to play an important role in physical exercise. However, its expression patterns and physiological effects in the central nuclei under different exercise states are not well understood. Five-week old male Sprague-Dawley rats were randomly divided into two groups of 21 each: Control and Exercise. Control rats were sedentary while Exercise rats were arranged to run on a treadmill (5-week adapting or moderate exercise and 2-week high-intensity exercise). Seven rats were taken from each group at day33, day42 and day49 for examination of blood biochemical parameters (lactate, Lac; blood urea nitrogen, BUN; glucose) and for detection of nuclei β-EP level with immunohistochemistry. The results showed that Lac and BUN levels were significant increased after the high intensity exercise. The five-week exercise caused a significantly increased β-EP in caudate putamen (CPu), amygdala, paraventricular thalamic nucleus (PVT), ventromedial hypothalamus nucleus (VMH) and gigantocellular reticular nucleus (Gi). The high intensity exercise induced an elevated β-EP in CPu and nucleus of the solitary tract (Sol), but a decreased β-EP in globus pallidus (GP). Compared with Control, exercise rats showed an elevated β-EP in CPu, PVT, VMH, accumbens nucleus, Gi and Sol, and a decreased β-EP in GP at day49. The β-EP levels in acurate nucleus, periadueductal gray and parabrachial nucleus were not changed at day33, 42 and 49. In conclusion, β-EP levels in different nuclei changed under the moderate and high intensity exercises, which may contribute to modifying exercise-produced psychological and physiological effects.
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Affiliation(s)
- Liang Xue
- Physical Education Department, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jinrui Sun
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jiandi Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yi Ding
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shuhuai Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mingxing Ding
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong Pei
- Physical Education Department, Huazhong Agricultural University, Wuhan 430070, China.
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Hougaard A, Nielsen SH, Gaist D, Puonti O, Garde E, Reislev NL, Iversen P, Madsen CG, Blaabjerg M, Nielsen HH, Krøigård T, Østergaard K, Kyvik KO, Madsen KH, Siebner HR, Ashina M. Migraine with aura in women is not associated with structural thalamic abnormalities. Neuroimage Clin 2020; 28:102361. [PMID: 32763831 PMCID: PMC7404547 DOI: 10.1016/j.nicl.2020.102361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Migraine with aura is a highly prevalent disorder involving transient neurological disturbances associated with migraine headache. While the pathophysiology is incompletely understood, findings from clinical and basic science studies indicate a potential key role of the thalamus in the mechanisms underlying migraine with and without aura. Two recent, clinic-based MRI studies investigated the volumes of individual thalamic nuclei in migraine patients with and without aura using two different data analysis methods. Both studies found differences of thalamic nuclei volumes between patients and healthy controls, but the results of the studies were not consistent. Here, we investigated whether migraine with aura is associated with changes in thalamic volume by analysing MRI data obtained from a large, cross-sectional population-based study which specifically included women with migraine with aura (N = 156), unrelated migraine-free matched controls (N = 126), and migraine aura-free co-twins (N = 29) identified from the Danish Twin Registry. We used two advanced, validated analysis methods to assess the volume of the thalamus and its nuclei; the MAGeT Brain Algorithm and a recently developed FreeSurfer-based method based on a probabilistic atlas of the thalamic nuclei combining ex vivo MRI and histology. These approaches were very similar to the methods used in each of the two previous studies. Between-group comparisons were corrected for potential effects of age, educational level, BMI, smoking, alcohol, and hypertension using a linear mixed model. Further, we used linear mixed models and visual inspection of data to assess relations between migraine aura frequency and thalamic nuclei volumes in patients. In addition, we performed paired t-tests to compare volumes of twin pairs (N = 29) discordant for migraine with aura. None of our analyses showed any between-group differences in volume of the thalamus or of individual thalamic nuclei. Our results indicate that the pathophysiology of migraine with aura does not involve alteration of thalamic volume.
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Affiliation(s)
- Anders Hougaard
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Silas Haahr Nielsen
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - David Gaist
- Department of Neurology, Odense University Hospital, Denmark, Odense, Denmark; Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oula Puonti
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Ellen Garde
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Nina Linde Reislev
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Pernille Iversen
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Camilla Gøbel Madsen
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Radiology, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
| | - Morten Blaabjerg
- Department of Neurology, Odense University Hospital, Denmark, Odense, Denmark; Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Helle Hvilsted Nielsen
- Department of Neurology, Odense University Hospital, Denmark, Odense, Denmark; Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas Krøigård
- Department of Neurology, Odense University Hospital, Denmark, Odense, Denmark; Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Kamilla Østergaard
- Department of Neurology, Odense University Hospital, Denmark, Odense, Denmark; Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Kirsten Ohm Kyvik
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Odense Patient data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Kristoffer Hougaard Madsen
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hartwig Roman Siebner
- Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Neurology, Copenhagen University Hospital Bispebjerg, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Messoud Ashina
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Yasui M, Oda K, Masuo S, Hosoda S, Katayama T, Maruyama JI, Takaya N, Takeshita N. Invasive growth of Aspergillus oryzae in rice koji and increase of nuclear number. Fungal Biol Biotechnol 2020; 7:8. [PMID: 32518660 PMCID: PMC7275602 DOI: 10.1186/s40694-020-00099-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/23/2020] [Indexed: 01/02/2023] Open
Abstract
Background 'Rice koji' is a solid culture of Aspergillus oryzae on steamed rice grains. Multiple parallel fermentation, wherein saccharification of rice by A. oryzae and alcohol fermentation by the budding yeast occur simultaneously, leads to the formation of a variety of ingredients of Japanese sake. In sake brewing, the degree of mycelial invasive growth into the steamed rice, called 'haze-komi', highly correlates with the digestibility and quality of rice koji, since the hyphae growing into the rice secrete amylases and digest starch. Results In this study, we investigated mycelial distribution of GFP-tagged A. oryzae in rice koji made with different types of rice, such as sake rice and eating rice, with 50 or 90% polishing rate to remove abundant proteins and lipids near the surface. In addition, we compared transcriptomes of A. oryzae in the different types of rice koji. Finally, we found that A. oryzae increases the nuclear number and hyphal width in the course of 1-3 days cultivation. Conclusions Our imaging analyses indicate that A. oryzae hyphae grew more deeply into 50% polished rice than 90% polished rice. The increases of nuclear number may be a selectively acquired characteristic for the high secretory capacity during the long history of cultivation of this species.
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Affiliation(s)
- Mizuki Yasui
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ken Oda
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046 Japan
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shuji Hosoda
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takuya Katayama
- Department of Biotechnology, Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichi Maruyama
- Department of Biotechnology, Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Naoki Takaya
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Zhang Y, An T, Frey S. Fast jet proper motion discovered in a blazar at z=4.72. Sci Bull (Beijing) 2020; 65:525-530. [PMID: 36659183 DOI: 10.1016/j.scib.2020.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/16/2019] [Accepted: 01/02/2020] [Indexed: 01/21/2023]
Abstract
High-resolution observations of high-redshift (z>4) radio quasars offer a unique insight into jet kinematics at early cosmological epochs, as well as constraints on cosmological model parameters. Due to the general weakness of extremely distant objects and the apparently slow structural changes caused by cosmological time dilation, only a couple of high-redshift quasars (HRQs) have been studied with parsec-scale resolutions, and with limited number of observing epochs. Here we report on very long baseline interferometry (VLBI) observations of a high-redshift blazar J1430 + 4204 (z=4.72) in the 8 GHz frequency band at five different epochs spanning 22 years. The source shows a compact core-jet structure with two jet components being identified within 3 milli-arcsecond (mas) scale. The long time span and multiple-epoch data allow for the kinematic studies of the jet components. That results in a jet proper motion of μ(J1) = 0.017 ± 0.002 mas a-1 and μ(J2) = 0.156 ± 0.015 mas a-1, respectively. For the fastest-moving outer jet component J2, the corresponding apparent transverse speed is (19.5±1.9)c. The inferred bulk jet Lorentz factor Γ=14.6±3.8 and viewing angle θ=2.2°±1.6° indicate highly relativistic beaming. The Lorentz factor and apparent proper motion are the highest measured to date among the z>4 jetted radio sources, while the jet kinematics is still consistent with the cosmological interpretation of quasar redshifts.
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Affiliation(s)
- Yingkang Zhang
- Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao An
- Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030, China; Key Laboratory of Radio Astronomy, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Sándor Frey
- Konkoly Observatory, Research Centre for Astronomy and Earth Sciences, Konkoly Thege Miklós út 15-17, H-1121 Budapest, Hungary
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25
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Lloyd D, Millet CO, Williams CF, Hayes AJ, Pope SJA, Pope I, Borri P, Langbein W, Olsen LF, Isaacs MD, Lunding A. Functional imaging of a model unicell: Spironucleus vortens as an anaerobic but aerotolerant flagellated protist. Adv Microb Physiol 2020; 76:41-79. [PMID: 32408947 DOI: 10.1016/bs.ampbs.2020.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Advances in optical microscopy are continually narrowing the chasm in our appreciation of biological organization between the molecular and cellular levels, but many practical problems are still limiting. Observation is always limited by the rapid dynamics of ultrastructural modifications of intracellular components, and often by cell motility: imaging of the unicellular protist parasite of ornamental fish, Spironucleus vortens, has proved challenging. Autofluorescence of nicotinamide nucleotides and flavins in the 400-580 nm region of the visible spectrum, is the most useful indicator of cellular redox state and hence vitality. Fluorophores emitting in the red or near-infrared (i.e., phosphors) are less damaging and more penetrative than many routinely employed fluors. Mountants containing free radical scavengers minimize fluorophore photobleaching. Two-photon excitation provides a small focal spot, increased penetration, minimizes photon scattering and enables extended observations. Use of quantum dots clarifies the competition between endosomal uptake and exosomal extrusion. Rapid motility (161 μm/s) of the organism makes high resolution of ultrastructure difficult even at high scan speeds. Use of voltage-sensitive dyes determining transmembrane potentials of plasma membrane and hydrogenosomes (modified mitochondria) is also hindered by intracellular motion and controlled anesthesia perturbs membrane organization. Specificity of luminophore binding is always questionable; e.g. cationic lipophilic species widely used to measure membrane potentials also enter membrane-bounded neutral lipid droplet-filled organelles. This appears to be the case in S. vortens, where Coherent Anti-Stokes Raman Scattering (CARS) micro-spectroscopy unequivocally images the latter and simultaneous provides spectral identification at 2840 cm-1. Secondary Harmonic Generation highlights the highly ordered structure of the flagella.
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Affiliation(s)
- David Lloyd
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom; School of Engineering, Cardiff, Wales, United Kingdom
| | - Coralie O Millet
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | | | - Anthony J Hayes
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Simon J A Pope
- School of Chemistry, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - Iestyn Pope
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Paola Borri
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Wolfgang Langbein
- School of Physics and Astronomy, Cardiff University, Cardiff, Wales, United Kingdom
| | - Lars Folke Olsen
- Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marc D Isaacs
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Anita Lunding
- Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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26
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Meador WD, Mathur M, Sugerman GP, Jazwiec T, Malinowski M, Bersi MR, Timek TA, Rausch MK. A detailed mechanical and microstructural analysis of ovine tricuspid valve leaflets. Acta Biomater 2020; 102:100-113. [PMID: 31760220 DOI: 10.1016/j.actbio.2019.11.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 12/26/2022]
Abstract
The tricuspid valve ensures unidirectional blood flow from the right atrium to the right ventricle. The three tricuspid leaflets operate within a dynamic stress environment of shear, bending, tensile, and compressive forces, which is cyclically repeated nearly three billion times in a lifetime. Ostensibly, the microstructural and mechanical properties of the tricuspid leaflets have mechanobiologically evolved to optimally support their function under those forces. Yet, how the tricuspid leaflet microstructure determines its mechanical properties and whether this relationship differs between the three leaflets is unknown. Here we perform a microstructural and mechanical analysis in matched ovine tricuspid leaflet samples. We found that the microstructure and mechanical properties vary among the three tricuspid leaflets in sheep. Specifically, we found that tricuspid leaflet composition, collagen orientation, and valve cell nuclear morphology are spatially heterogeneous and vary across leaflet type. Furthermore, under biaxial tension, the leaflets' mechanical behaviors exhibited unequal degrees of mechanical anisotropy. Most importantly, we found that the septal leaflet was stiffer in the radial direction and not the circumferential direction as with the other two leaflets. The differences we observed in leaflet microstructure coincide with the varying biaxial mechanics among leaflets. Our results demonstrate the structure-function relationship for each leaflet in the tricuspid valve. We anticipate our results to be vital toward developing more accurate, leaflet-specific tricuspid valve computational models. Furthermore, our results may be clinically important, informing differential surgical treatments of the tricuspid valve leaflets. Finally, the identified structure-function relationships may provide insight into the homeostatic and remodeling potential of valvular cells in altered mechanical environments, such as in diseased or repaired tricuspid valves. STATEMENT OF SIGNIFICANCE: Our work is significant as we investigated the structure-function relationship of ovine tricuspid valve leaflets. This is important as tricuspid valves fail frequently and our current approach to repairing them is suboptimal. Specifically, we related the distribution of structural and cellular elements, such as collagen, glycosaminoglycans, and cell nuclei, to each leaflet's mechanical properties. We found that leaflets have different structures and that their mechanics differ. This may, in the future, inform leaflet-specific treatment strategies and help optimize surgical outcomes.
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Affiliation(s)
- William D Meador
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78705, USA
| | - Mrudang Mathur
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78705, USA
| | - Gabriella P Sugerman
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78705, USA
| | - Tomasz Jazwiec
- Cardiothoracic Surgery, Spectrum Health, Grand Rapids, MI 49503, USA; Department of Cardiac, Vascular, and Endovascular Surgery and Transplantology, Medical University of Silesia School of Medicine in Katowice, Silesian Centre for Heart Diseases, Zabrze, Poland
| | - Marcin Malinowski
- Cardiothoracic Surgery, Spectrum Health, Grand Rapids, MI 49503, USA; Department of Cardiac Surgery, Medical University of Silesia School of Medicine in Katowice, Katowice, Poland
| | - Matthew R Bersi
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Tomasz A Timek
- Cardiothoracic Surgery, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Manuel K Rausch
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78705, USA; Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78705, USA; Department of Aerospace Engineering and Engineering Mechanics, The University of Texas at Austin, Austin, TX 78705, USA.
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27
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Abstract
Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a widely used method for mapping the genome-wide locations of chromatin-associated proteins. This protocol has been developed and utilized to perform ChIP on histone covalent modifications in various plant species including cereals. DNA and chromatin-associated proteins are crosslinked with formaldehyde. Chromatin is then isolated from nuclei and sheared via sonication. Antibodies targeting the histone modification of interest are incubated with the sheared chromatin and nonspecific interactions are washed away. DNA is purified via phenol-chloroform extraction, end-repaired, ligated to sequencing adapters, and PCR-amplified.
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28
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Rabinovich PM, Zhang J, Kerr SR, Cheng BH, Komarovskaya M, Bersenev A, Hurwitz ME, Krause DS, Weissman SM, Katz SG. A versatile flow-based assay for immunocyte-mediated cytotoxicity. J Immunol Methods 2019; 474:112668. [PMID: 31525367 DOI: 10.1016/j.jim.2019.112668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022]
Abstract
Cell-mediated cytotoxicity is a critical function of the immune system in mounting defense against pathogens and cancers. Current methods that allow direct evaluation of cell-mediated cytotoxicity suffer from a wide-range of drawbacks. Here, we present a novel strategy to measure cytotoxicity that is direct, sensitive, rapid, and highly adaptable. Moreover, it allows accurate measurement of viability of both target and effector cells. Target cells are fluorescently labeled with a non-toxic, cell-permeable dye that covalently binds to cell proteins, including nuclear proteins. The labeled target cells are incubated with effector cells to begin killing. Following the killing reaction, the cell mixture is incubated with another dye that specifically stains proteins of dead cells, including nuclear proteins. In the final step, cell nuclei are released by Triton X-100, and analyzed by flow cytometry. This results in four nuclear staining patterns that separate target and effector nuclei as well as nuclei of live and dead cells. Analyzing nuclei, instead of cells, greatly reduces flow cytometry errors caused by the presence of target-effector cell aggregates. Target killing time can often be reduced to 2 h and the assay can be done in a high throughput format. We have successfully validated this assay in a variety of cytotoxicity scenarios including those mediated by NK-92 cells, Chimeric Antigen Receptor (CAR)-T cells, and Tumor Infiltrating Lymphocytes (TIL). Therefore, this technique is broadly applicable, highly sensitive and easily administered, making it a powerful tool to assess immunotherapy-based, cell-mediated cytotoxicity.
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Affiliation(s)
- Peter M Rabinovich
- Department of Pathology, Yale School of Medicine, New Haven, CT 06525, USA
| | - Jialing Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06525, USA
| | - Samuel R Kerr
- Department of Pathology, Yale School of Medicine, New Haven, CT 06525, USA
| | - Bao-Hui Cheng
- Department of Pathology, Yale School of Medicine, New Haven, CT 06525, USA
| | - Marina Komarovskaya
- Department of Laboratory Medicine, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06525, USA
| | - Alexey Bersenev
- Department of Laboratory Medicine, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06525, USA
| | - Michael E Hurwitz
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06525, USA; Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT 06525, USA
| | - Diane S Krause
- Department of Pathology, Yale School of Medicine, New Haven, CT 06525, USA; Department of Laboratory Medicine, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06525, USA; Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT 06525, USA
| | - Sherman M Weissman
- Department of Genetics, Yale School of Medicine, New Haven, CT 06525, USA
| | - Samuel G Katz
- Department of Pathology, Yale School of Medicine, New Haven, CT 06525, USA; Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT 06525, USA.
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29
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Abstract
Photoreceptor cells (PRCs) mature from simple epithelial cells, a process characterised by growth and compartmentalisation of the apical membrane into an inner and an outer segment. So far, a PRC subtype-specific description of morphological and cellular changes in the developing zebrafish retina is missing. Here, we performed an in-depth characterisation of four of the five PRC subtypes of the zebrafish retina between 51 and 120 h post fertilisation, including quantification of the size of different compartments, localisation of polarity proteins and positioning of organelles. One of the major findings was the anisotropic and subtype-specific growth of the different PRC compartments. In addition, a transient accumulation of endoplasmic reticulum in rod PRCs, changes in chromatin organisation in UV sensitive cones and differential expression of polarity proteins during the initial stages of PRC maturation were observed. The results obtained provide a developmental timeline that can be used as a platform for future studies on PRC maturation and function. This platform was applied to document that increased exposure to light leads to smaller apical domains of PRCs. Summary: We characterised subtype-specific growth of the different photoreceptor compartments, organelle distribution and the influence of light on the growth of the apical membrane.
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Affiliation(s)
- Cátia Crespo
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Elisabeth Knust
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
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30
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Zhou Y, Li H, Zhang W, Xu J, Li X, Ji B. Automatic directional analysis of cell fluorescence images and morphological modeling of microfilaments. Med Biol Eng Comput 2018; 57:325-337. [PMID: 30117068 DOI: 10.1007/s11517-018-1871-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 06/15/2018] [Indexed: 11/25/2022]
Abstract
Cytoskeleton and nucleus are two important anatomic components in eukaryotic cells. Cell fluorescence images are employed to study their realignment and deformation during cell extrusion. Quantitative analysis and modeling of cell orientation are investigated in this paper. For orientation measurement, alignment orientation of microfilaments is calculated using structure tensor method. Nuclei is segmented and fitted to ellipses in nuclei images. Based on the fitted ellipse, orientation and aspect ratio of each nucleus are computed. A morphological model is proposed to describe the movement of microfilaments quantitatively. The parameters of the model are determined by in-plane stresses obtained by numerical simulation. The proposed automatic orientation measurement algorithms can help to analyze the relationship between cell orientation and stress qualitatively. The proposed morphological model is the first model to quantitatively describe the relationship of microfilament movement with stress. Experimental results show that cell and nucleus tend to align along in-plane maximum shear stress and the proposed morphological model is a reasonable model for cell movement. The modeling of cell behavior under different stress can facilitate biomedical research such as tissue engineering and cancer analysis. Graphical abstract ᅟ.
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Affiliation(s)
- Yue Zhou
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Huiqi Li
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, China.
| | - Wanjun Zhang
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Jiayi Xu
- School of Aerospace Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaojun Li
- School of Aerospace Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Baohua Ji
- School of Aerospace Engineering, Beijing Institute of Technology, Beijing, 100081, China
- Department of Engineering Mechanics, Zhejiang University, Zhejiang, 310027, China
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31
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Chen J, Teo BHD, Lu J. A Method for Extracting the Nuclear Scaffold from the Chromatin Network. Bio Protoc 2018; 8:e2821. [PMID: 34286031 DOI: 10.21769/bioprotoc.2821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 11/02/2022] Open
Abstract
Each cell contains many large DNA polymers packed in a nucleus of approx. 10 μm in diameter. With histones, these DNA polymers are known to form chromatins. How chromatins further compact in the nucleus is unclear but it inevitably depends on an extensive non-chromatin nuclear scaffold. Imaging of endogenous chromatin network and the complementary scaffold that support this network has not been achieved but biochemical and proteomic investigations of the scaffold can still provide important insights into this chromatin-organizing network. However, this demands highly inclusive and reproducible extraction of the nuclear scaffold. We have recently developed a simple protocol for releasing the scaffold components from chromatins. The inclusiveness of the extract was testified by the observation that, upon its extraction from the nuclei, the remaining nuclear chromatins were liberated into extended and often parallel chromatin fibers. Basically, this protocol includes the generation of pure nuclei, treatment of the nuclei with Triton X-100 to generate envelope-depleted nuclei (TxN), and extraction of the nuclei at 500 mM NaCl in a sucrose-containing buffer. This combined extract of TxN is known as TxNE.
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Affiliation(s)
- Junjie Chen
- Department of Microbiology, Yong Loo Lin School of Medicine, Immunology Program, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology, Yong Loo Lin School of Medicine, Immunology Program, National University of Singapore, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology, Yong Loo Lin School of Medicine, Immunology Program, National University of Singapore, Singapore, Singapore
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32
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Abstract
Brain metabolic DNA (BMD) is not involved in cell division or DNA repair but is modulated by memory acquisition, sleep processing, and circadian oscillations. Using routine methods of subcellular fractionation, newly synthesized BMD from male rats is shown to be localized in crude nuclear, mitochondrial, and microsomal fractions and in two fractions of purified nuclei. Sub-fractionation of the mitochondrial fraction indicates the prevalent localization of BMD in free mitochondria and to a lesser degree in synaptosomes and myelin. Cesium density profiles of homogenate, subcellular fractions, and purified nuclei obtained after incorporation periods from 30 min to 4 h indicate that BMD synthesis takes place by reverse transcription in cytoplasmic organelles. Following the acquisition of the double-stranded structure, BMD is transferred to nuclei. Kinetic analyses lasting several weeks highlight the massive BMD turnover in subcellular fractions and purified nuclei and its dependence on age. Data are in agreement with the role of BMD as a temporary information store of cell responses of potential use in comparable forthcoming experiences.
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33
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Abstract
Programmed cell death (PCD) is a key process for the development and differentiation of multicellular organisms, which is characterized by well-defined morphological and biochemical features. These include chromatin condensation, DNA degradation and nuclear fragmentation, with nucleases and proteases playing a relevant function in these processes. In this chapter we describe methods routinely used for the analysis of hallmarks of developmentally regulated PCD in cereal seed tissues, which are based on agarose and polyacrylamide gel electrophoresis, in situ staining of DNA fragmentation, and cell-free assays of relevant enzymatic activities.
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34
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Xu Y, Gan ES, Ito T. In Situ Proximity Ligation Assay to Detect the Interaction Between Plant Transcription Factors and Other Regulatory Proteins. Methods Mol Biol 2018; 1830:325-335. [PMID: 30043379 DOI: 10.1007/978-1-4939-8657-6_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In plants, a lot of transcription factors fulfill their roles in gene regulation through the interaction with other regulatory proteins and co-factors. Thus, confirmation of protein-protein interaction is key to understand the precise function of transcription factors. Many methods have been developed to investigate the protein-protein interaction in vivo and in vitro. In situ Proximity Ligation Assay (PLA) is an innovative method to test protein-protein interaction in your tissues or cells of interest in vivo. Furthermore, this method allows us to detect transient interaction and low-abundance protein interaction with single molecule resolution. In this chapter, we describe a detailed protocol for the study of interaction between plant transcription factors and other regulatory proteins, in the scale of single nuclei of plant organ, tissues and cells.
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Affiliation(s)
- Yifeng Xu
- Temasek Life Sciences Laboratory (TLL), 1 Research Link, National University of Singapore, Singapore, Singapore.,Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Eng-Seng Gan
- Temasek Life Sciences Laboratory (TLL), 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Toshiro Ito
- Temasek Life Sciences Laboratory (TLL), 1 Research Link, National University of Singapore, Singapore, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore. .,Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
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35
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Prusov AN, Kolomijtseva GY, Smirnova TA. Differential scanning calorimetric study of antibiotic distamycin A binding with chromatin within isolated rat liver nuclei. Pharm Biol 2017; 55:687-690. [PMID: 27982735 PMCID: PMC6130587 DOI: 10.1080/13880209.2016.1258427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CONTEXT Natural oligopeptide antibiotic distamycin A (Dst) biosynthesized by Streptomyces distallicus is traditionally used in medical practice as an anti-inflammatory and antitumour drug. OBJECTIVE Dst was investigated for its effect on the structural components of native chromatin directly within isolated rat liver nuclei in the presence of physiologically significant cations (magnesium or spermine and spermidine). MATERIALS AND METHODS Differential scanning calorimetry (DSC) was used to study the Dst action at molar ratio Dst/DNA = 0.1 and 0.15 mM Dst on the melting profile of nuclei suspension in different conditions. RESULTS Results showed that the thermodynamic parameters of control nuclei in the presence of polyamines or Mg2+ were different. The incubation of nuclei with Dst raised transition temperatures of relaxed (peak II) and topologically constrained DNA (peak III) by 6-8 °C and decreased by 2-4 °C that of core-histones (peak I). The total excess transition enthalpy (ΔHexc) in buffer with polyamines (24.7 kJ/mol DNA nucleotides) increased by1.5 times versus control but in buffer with Mg2+, the value of ΔHexc (35.8 kJ/mol DNA nucleotides) remained unchanged. CONCLUSIONS The association of Dst with chromatin in the nucleus weakens histone-DNA contacts and causes additional strengthening of interaction between two complementary DNA chains. Our results contribute towards validation of DSC to test drug ability to modulate chromatin structure in the physiological environment and to clarify the mechanism of these modulations.
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Affiliation(s)
- Andrey N. Prusov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- CONTACT Andrey N. PrusovM.V. Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Leninskie Gory 1, Bldg. 40, Moscow119991, Russia
| | - Galina Ya. Kolomijtseva
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana A. Smirnova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
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36
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Galbraith DW, Sliwinska E, Samadder P. Nuclear Cytometry: Analysis of the Patterns of DNA Synthesis and Transcription Using Flow Cytometry, Confocal Microscopy, and RNA Sequencing. Methods Mol Biol 2017; 1678:371-392. [PMID: 29071687 DOI: 10.1007/978-1-4939-7346-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Eukaryotes are defined by cells that contain a nucleus and other membrane-bound organelles. Cytometric analysis in situ, utilizing imaging, provides a useful understanding of the structure and function of the various subcellular components, particularly when combined with methods that preserve the living state. In terms of information provided by the observation of eukaryotic nuclei, imaging has provided a wealth of information about cellular multiplication. When organisms are present in multicellular form (tissues and organs), this property does not generally confound imaging cytometry. Multicellular eukaryotic species present immediate problems when being considered for analysis using flow cytometry which requires suspensions of single particles. Although some eukaryotic cell types exist as natural single cell suspensions (cf. the erythropoietic system), for other tissues and organs, strategies are required to produce single particle suspensions. This chapter illustrates the application of flow cytometry combined with confocal microscopy to analyze complex organs, focusing on properties of the plant nucleus, and then goes on to describe how suspensions of nuclei can be prepared from tissues and organs, and used for flow cytometric analysis of cellular and transcriptional states. The application of these techniques to animal species is also discussed with the implication that this strategy is universally applicable for the characterization of nuclei within tissues that cannot readily be converted into suspensions of cells.
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Affiliation(s)
- David W Galbraith
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA.
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics, Physiology and Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Partha Samadder
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA
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37
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Abstract
Specific labeling of proteins and nucleic acids by immunofluorescence or in situ techniques is an important adjunct to microscopical analysis for cell biology. Labeling of nuclear structures in intact complex tissues is often hampered by problems of penetration of the macromolecular labeling reagents needed. Here we describe a method of labeling isolated plant nuclei that we have found to be a useful approach that can help to overcome these problems.
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38
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Wang L, Xu XB, You WW, Lin XX, Li CT, Qian HR, Zhang LH, Yang Y. The cytoplasmic nuclear shuttling of Beclin 1 in neurons with Alzheimer's disease-like injury. Neurosci Lett 2017; 661:63-70. [PMID: 28964771 DOI: 10.1016/j.neulet.2017.09.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/08/2017] [Accepted: 09/26/2017] [Indexed: 01/05/2023]
Abstract
The abnormal expression of the autophagy-related protein Beclin 1 has been implicated in Alzheimer's disease (AD) brains, whereas the precise involvement of Caspase-mediated Beclin 1 cleavage in AD neurons has not yet been fully clarified. In this study, we investigated the distribution of Beclin 1 fragments in neurons with AD-like injury. Our results demonstrated that Beclin 1 was expressed in neurons but not in astrocytes in both neuron-glia co-cultures and in cortical tissue slices. The full length and C-terminal fragments of human Beclin 1 was mainly expressed in cytoplasm, while the N-terminal fragment of Beclin 1 was predominantly localized in nucleus. Compared to amyloid-β (Aβ)42-1 treatment control, exposure of PC12 cells or cortical neurons to Aβ1-42 resulted in cell injury, with the appearance of neuritic shortening, reduced nuclear diameter in PC12 cells, beading formation and fragmentation in cortical neurons. A partial nuclear translocation of Beclin 1 was detected in cells incubated with Aβ1-42, which could be inhibited by the administration of pan-Caspase inhibitor or Caspase 3 specific inhibitor. Moreover, Beclin 1 mutation at 146/149 sites was resistant to Aβ1-42-induced nuclear translocation. The nuclear translocation of Beclin 1 could also been detected in the brains of 12-month-old APPSwe/PS1dE9 transgenic mice. Our findings suggest that after Caspase 3-mediated Beclin 1 cleavage at 146/149 sites, the N-terminal fragments of Beclin 1 may partially translocate into nuclei in neurons subjected to AD-like injury.
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Affiliation(s)
- Li Wang
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Xiao-Bin Xu
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Wen-Wen You
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Xiao-Xia Lin
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng-Tan Li
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Hao-Ran Qian
- Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou 310016, China
| | - Li-Hui Zhang
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China.
| | - Yi Yang
- Department of Pharmacology, Hangzhou Key Laboratory of Medical Neurobiology, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China.
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Saia-Cereda VM, Santana AG, Schmitt A, Falkai P, Martins-de-Souza D. The Nuclear Proteome of White and Gray Matter from Schizophrenia Postmortem Brains. Mol Neuropsychiatry 2017; 3:37-52. [PMID: 28879200 DOI: 10.1159/000477299] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Schizophrenia (SCZ) is a serious neuropsychiatric disorder that manifests through several symptoms from early adulthood. Numerous studies over the last decades have led to significant advances in increasing our understanding of the factors involved in SCZ. For example, mass spectrometry-based proteomic analysis has provided important insights by uncovering protein dysfunctions inherent to SCZ. Here, we present a comprehensive analysis of the nuclear proteome of postmortem brain tissues from corpus callosum (CC) and anterior temporal lobe (ATL). We show an overview of the role of deregulated nuclear proteins in these two main regions of the brain: the first, mostly composed of glial cells and axons of neurons, and the second, represented mainly by neuronal cell bodies. These samples were collected from SCZ patients in an attempt to characterize the role of the nucleus in the disease process. With the ATL nucleus enrichment, we found 224 proteins present at different levels, and 76 of these were nuclear proteins. In the CC analysis, we identified 119 present at different levels, and 24 of these were nuclear proteins. The differentially expressed nuclear proteins of ATL are mainly associated with the spliceosome, whereas those of the CC region are associated with calcium/calmodulin signaling.
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Affiliation(s)
- Verônica M Saia-Cereda
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Aline G Santana
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University (LMU), Munich, Germany.,Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, University of São Paulo, São Paulo, Brazil
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University (LMU), Munich, Germany
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,UNICAMP's Neurobiology Center, Campinas, Brazil
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Kilaru S, Schuster M, Ma W, Steinberg G. Fluorescent markers of various organelles in the wheat pathogen Zymoseptoria tritici. Fungal Genet Biol 2017; 105:16-27. [PMID: 28579390 PMCID: PMC5536155 DOI: 10.1016/j.fgb.2017.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/05/2017] [Accepted: 05/06/2017] [Indexed: 12/22/2022]
Abstract
17 vectors are described that allow labelling of 7 subcellular structures. The fluorescent markers target the plasma membrane, endoplasmic reticulum, nucleus. Markers also target the actin cytoskeleton, peroxisomes and autophagosomes. These markers complete are toolkit of fluorescent reporters. Reporters allow cell biological studies in the Septoria tritici blotch fungus.
Development of novel strategies to control fungal plant pathogens requires understanding of their cellular organisation and biology. Live cell imaging of fluorescent organelle markers has provided valuable insight into various aspects of their cell biology, including invasion strategies in plant pathogenic fungi. Here, we introduce a set of 17 vectors that encode fluorescent markers to visualize the plasma membrane, endoplasmic reticulum (ER), chromosomes, the actin cytoskeleton, peroxisomes and autophagosomes in the wheat pathogen Zymoseptoria tritici. We fused either enhanced green-fluorescent protein (eGFP) or a codon-optimised version of GFP (ZtGFP) to homologues of a plasma membrane-located Sso1-like syntaxin, an ER signalling and retention peptide, a histone H1 homologue, the LifeAct actin-binding peptide, a mitochondrial acetyl-CoA dehydrogenase, a peroxisomal import signal and a homologue of the ubiquitin-like autophagosomal protein Atg8. We expressed these markers in wildtype strain IPO323 and confirmed the specificity of these markers by counterstaining or physiological experiments. This new set of molecular tools will help understanding the cell biology of the wheat pathogen Z. tritici.
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Affiliation(s)
- S Kilaru
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - M Schuster
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - W Ma
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - G Steinberg
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK; University of Utrecht, Department of Biology, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Cobia DJ, Smith MJ, Salinas I, Ng C, Gado M, Csernansky JG, Wang L. Progressive deterioration of thalamic nuclei relates to cortical network decline in schizophrenia. Schizophr Res 2017; 180:21-27. [PMID: 27613507 PMCID: PMC5263051 DOI: 10.1016/j.schres.2016.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 01/28/2023]
Abstract
Thalamic abnormalities are considered part of the complex pathophysiology of schizophrenia, particularly the involvement of specific thalamic nuclei. The goals of this study were to: introduce a novel atlas-based parcellation scheme for defining various thalamic nuclei; compare their integrity in a schizophrenia sample against healthy individuals at baseline and follow-up time points, as well as rates of change over time; examine relationships between the nuclei and abnormalities in known connected cortical regions; and finally, to determine if schizophrenia-related thalamic nuclei changes relate to cognitive functioning and clinical symptoms. Subjects were from a larger longitudinal 2-year follow-up study, schizophrenia (n=20) and healthy individuals (n=20) were group-matched for age, gender, and recent-alcohol use. We used high-dimensional brain mapping to obtain thalamic morphology, and applied a novel atlas-based method for delineating anterior, mediodorsal, and pulvinar nuclei. Results from cross sectional GLMs revealed group differences in bilateral mediodorsal and anterior nuclei, while longitudinal models revealed significant group-by-time interactions for the mediodorsal and pulvinar nuclei. Cortical correlations were the strongest for the pulvinar in frontal, temporal and parietal regions, followed by the mediodorsal nucleus in frontal regions, but none in the anterior nucleus. Thalamic measures did not correlate with cognitive and clinical scores at any time point or longitudinally. Overall, findings revealed a pattern of persistent progressive abnormalities in thalamic nuclei that relate to advancing cortical decline in schizophrenia, but not with measures of behavior.
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Affiliation(s)
- Derin J. Cobia
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 446 E. Ontario, Suite 7-100, Chicago, IL 60611 USA
| | - Matthew J. Smith
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 446 E. Ontario, Suite 7-100, Chicago, IL 60611 USA
| | - Ilse Salinas
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 446 E. Ontario, Suite 7-100, Chicago, IL 60611 USA
| | - Charlene Ng
- Virginia Commonwealth University, Chesterfield Family Practice Center, 2500 Pocoshock Place, Suite 202, Richmond, VA 23235 USA
| | - Mohktar Gado
- Department of Radiology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110 USA
| | - John G. Csernansky
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 446 E. Ontario, Suite 7-100, Chicago, IL 60611 USA
| | - Lei Wang
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 446 E. Ontario, Suite 7-100, Chicago, IL 60611 USA,Department of Radiology, Northwestern University Feinberg School of Medicine, 446 E. Ontario, Suite 7-100, Chicago, IL 60611 USA
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Abstract
Here we describe methods for producing nuclei from Arabidopsis suspension cultures or root tips of Arabidopsis, wheat, or pea. These methods could be adapted for other species and cell types. The resulting nuclei can be further purified for use in biochemical or proteomic studies, or can be used for microscopy. We also describe how the nuclei can be used to obtain a preparation of nucleoli.
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Affiliation(s)
- Alison F Pendle
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Peter J Shaw
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
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Bai L, Lin W, Wu P, Deng J, Li C, Xu D, Wang D, Chen L. Memory effect and redistribution of cavitation nuclei in a thin liquid layer. Ultrason Sonochem 2016; 32:213-217. [PMID: 27150763 DOI: 10.1016/j.ultsonch.2016.02.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/30/2016] [Accepted: 02/26/2016] [Indexed: 06/05/2023]
Abstract
Temporal evolution and spatial distribution of acoustic cavitation structures in a thin liquid layer were investigated experimentally with high-speed photography. The inception and disappearance processes of cavitation bubble cloud revealed that the metastable cavitaton structures formed in the thin liquid layer caused a long-term "memory effect". A factor which weakens the memory effect was identified. The distribution of cavitation nuclei was investigated by changing the temporal decay of the memory effect.
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Affiliation(s)
- Lixin Bai
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Weijun Lin
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
| | - Pengfei Wu
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jingjun Deng
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
| | - Chao Li
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
| | - Delong Xu
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
| | - Dong Wang
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
| | - Lishuo Chen
- Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China
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Gaveglio VL, Pascual AC, Giusto NM, Pasquaré SJ. Age-related changes in retinoic, docosahexaenoic and arachidonic acid modulation in nuclear lipid metabolism. Arch Biochem Biophys 2016; 604:121-7. [PMID: 27355428 DOI: 10.1016/j.abb.2016.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/08/2016] [Accepted: 06/24/2016] [Indexed: 12/26/2022]
Abstract
The aim of this work was to study how age-related changes could modify several enzymatic activities that regulate lipid mediator levels in nuclei from rat cerebellum and how these changes are modulated by all-trans retinoic acid (RA), docosahexaenoic acid (DHA) and arachidonic acid (AA). The higher phosphatidate phosphohydrolase activity and lower diacylglycerol lipase (DAGL) activity observed in aged animals compared with adults could augment diacylglycerol (DAG) availability in the former. Additionally, monoacylglycerol (MAG) availability could be high due to an increase in lysophosphatidate phosphohydrolase (LPAPase) activity and a decrease in monocylglycerol lipase activity. Interestingly, RA, DHA and AA were observed to modulate these enzymatic activities and this modulation was found to change in aged rats. In adult nuclei, whereas RA led to high DAG and MAG production through inhibition of their hydrolytic enzymes, DHA and AA promoted high MAG production by LPAPase and DAGL stimulation. In contrast, in aged nuclei RA caused high MAG generation whereas DHA and AA diminished it through LPAPase activity modulation. These results demonstrate that aging promotes a different nuclear lipid metabolism as well as a different type of non-genomic regulation by RA, DHA and AA, which could be involved in nuclear signaling events.
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Affiliation(s)
- Virginia L Gaveglio
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ana C Pascual
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Norma M Giusto
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Susana J Pasquaré
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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Xiong H, Du S, Ni J, Zhou J, Yao J. Mitochondria and nuclei dual-targeted heterogeneous hydroxyapatite nanoparticles for enhancing therapeutic efficacy of doxorubicin. Biomaterials 2016; 94:70-83. [PMID: 27105438 DOI: 10.1016/j.biomaterials.2016.04.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/02/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022]
Abstract
Dual-targeted nanoparticles have been increasingly used to realize greater anti-proliferation effect by attacking double key sites of tumor cells. In order to retain nuclei inhibition effect and enhance DOX-induced apoptosis by mitochondrial pathway simultaneously, hyaluronic acid (HA) modified hydroxyapatite (HAP) nanoparticles (HAP-HA), the functional calcium-based tumor targeting nanoparticles, have been developed. In this nanosystem, HA acts as an active tumor-targeting ligand to bind the CD44 receptors which are overexpressed on the surface of tumor cells while HAP can load and deliver DOX to both nuclei and mitochondria of tumor cells. In this study, DOX-loaded HAP-HA nanoparticles (DOX/HAP-HA) exhibited satisfactory drug loading efficiency which was up to 214.55 ± 51.05 μg mg(-1) and showed a uniform nano-scaled particle size. The mitochondrial and nuclei targetability of DOX/HAP-HA was confirmed by confocal laser scanning microscopy analyses. Besides, western blot assay demonstrated that DOX/HAP-HA could markedly enhance mitochondrial cytochrome C leakage and thereby activate apoptotic cascade associated with it. In addition, in vivo anti-tumor efficacy and toxicity evaluation of DOX/HAP-HA indicated that DOX/HAP-HA was more effective and less harmful compared to other groups. DOX/HAP-HA might be a new promising targeted delivery system for effective cancer therapy.
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Affiliation(s)
- Hui Xiong
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Shi Du
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jiang Ni
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jianping Zhou
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jing Yao
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China.
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Pascual J, Alegre S, Nagler M, Escandón M, Annacondia ML, Weckwerth W, Valledor L, Cañal MJ. The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata. J Proteomics 2016; 143:390-400. [PMID: 26961940 DOI: 10.1016/j.jprot.2016.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 12/31/2022]
Abstract
UNLABELLED The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows. The combination of SEQUEST, de novo sequencing, and novel annotation pipelines allowed cover sensing and transduction pathways, endoplasmic reticulum-related mechanisms and the regulation of chromatin dynamism and gene expression by histones, histone-like NF-Ys, and other transcription factors previously unrelated to this stress source, as well as the role of alternative splicing and other mechanisms involved in RNA translation and protein synthesis. The determination of 33 transcription factors, including NF-YB13, Pp005698_3 (NF-YB) and Pr009668_2 (WD-40), which are correlated to stress responsive mechanisms like an increased accumulation of photoprotective pigments and reduced photosynthesis, pointing them as strong candidate biomarkers for breeding programs aimed to improve UV resistance of pine trees. SIGNIFICANCE The description of the nuclear proteome of Pinus radiata combining a classic approach based on the use of SEQUEST and the use of a mass accuracy precursor alignment (MAPA) allowed an unprecedented protein coverage. This workflow provided the methodological basis for characterizing the changes in the nuclear proteome triggered by UV irradiation, allowing the depiction of the nuclear events involved in stress response and adaption. The relevance of some of the discovered proteins will suppose a major advance in stress biology field, also providing a set of transcription factors that can be considered as strong biomarker candidates to select trees more tolerant to UV radiation in forest upgrade programs.
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Rausch A, Zhang W, Haak KV, Mennes M, Hermans EJ, van Oort E, van Wingen G, Beckmann CF, Buitelaar JK, Groen WB. Altered functional connectivity of the amygdaloid input nuclei in adolescents and young adults with autism spectrum disorder: a resting state fMRI study. Mol Autism 2016; 7:13. [PMID: 26823966 PMCID: PMC4730628 DOI: 10.1186/s13229-015-0060-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/07/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Amygdala dysfunction is hypothesized to underlie the social deficits observed in autism spectrum disorders (ASD). However, the neurobiological basis of this hypothesis is underspecified because it is unknown whether ASD relates to abnormalities of the amygdaloid input or output nuclei. Here, we investigated the functional connectivity of the amygdaloid social-perceptual input nuclei and emotion-regulation output nuclei in ASD versus controls. METHODS We collected resting state functional magnetic resonance imaging (fMRI) data, tailored to provide optimal sensitivity in the amygdala as well as the neocortex, in 20 adolescents and young adults with ASD and 25 matched controls. We performed a regular correlation analysis between the entire amygdala (EA) and the whole brain and used a partial correlation analysis to investigate whole-brain functional connectivity uniquely related to each of the amygdaloid subregions. RESULTS Between-group comparison of regular EA correlations showed significantly reduced connectivity in visuospatial and superior parietal areas in ASD compared to controls. Partial correlation analysis revealed that this effect was driven by the left superficial and right laterobasal input subregions, but not the centromedial output nuclei. CONCLUSIONS These results indicate reduced connectivity of specifically the amygdaloid sensory input channels in ASD, suggesting that abnormal amygdalo-cortical connectivity can be traced down to the socio-perceptual pathways.
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Affiliation(s)
- Annika Rausch
- Department of Cognitive Neuroscience, Radboud University Medical Center Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands ; Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands
| | - Wei Zhang
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands
| | - Koen V Haak
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands
| | - Maarten Mennes
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands
| | - Erno J Hermans
- Department of Cognitive Neuroscience, Radboud University Medical Center Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands ; Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands
| | - Erik van Oort
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands ; MIRA Institute, University of Twente, Enschede, The Netherlands
| | - Guido van Wingen
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands ; Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Christian F Beckmann
- Department of Cognitive Neuroscience, Radboud University Medical Center Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands ; Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands ; Centre for Functional MRI of the Brain (FMRIB), University of Oxford, Oxford, United Kingdom
| | - Jan K Buitelaar
- Department of Cognitive Neuroscience, Radboud University Medical Center Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands ; Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands ; Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Wouter B Groen
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands ; Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
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de Souza Junior JDA, de Sa MFG, Engler G, Engler JDA. Imaging Nuclear Morphology and Organization in Cleared Plant Tissues Treated with Cell Cycle Inhibitors. Methods Mol Biol 2016; 1370:59-68. [PMID: 26659954 DOI: 10.1007/978-1-4939-3142-2_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Synchronization of root cells through chemical treatment can generate a large number of cells blocked in specific cell cycle phases. In plants, this approach can be employed for cell suspension cultures and plant seedlings. To identify plant cells in the course of the cell cycle, especially during mitosis in meristematic tissues, chemical inhibitors can be used to block cell cycle progression. Herein, we present a simplified and easy-to-apply protocol to visualize mitotic figures, nuclei morphology, and organization in whole Arabidopsis root apexes. The procedure is based on tissue clearing, and fluorescent staining of nuclear DNA with DAPI. The protocol allows carrying out bulk analysis of nuclei and cell cycle phases in root cells and will be valuable to investigate mutants like overexpressing lines of genes disturbing the plant cell cycle.
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Affiliation(s)
- José Dijair Antonino de Souza Junior
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Av. W5 Norte final, Brasília, DF, 70770-900, Brazil
| | - Maria Fatima Grossi de Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Av. W5 Norte final, Brasília, DF, 70770-900, Brazil
| | - Gilbert Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, Sophia-Antipolis, France
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, Sophia-Antipolis, France.
- Institut Sophia Agrobiotech, 400 route des Chappes, BP 167, Sophia-Antipolis, Cedex, 0690, France.
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Roesslein M, Froehlich C, Miltenberger V, Ulbrich F, Goebel U, Loop T. Thiopental protects human neuroblastoma cells from apoptotic cell death - Potential role of heat shock protein 70. Life Sci 2015; 139:40-5. [PMID: 26297444 DOI: 10.1016/j.lfs.2015.07.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/09/2015] [Accepted: 07/30/2015] [Indexed: 11/23/2022]
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Abstract
Synucleins are small, soluble proteins expressed primarily in neural tissue and in certain tumors. The synuclein family consists of three members: α-, β-, and γ-synucleins present only in vertebrates. Members of the synuclein family have high sequence identity, especially in the N-terminal regions. The synuclein gene family came into the spotlight, when one of its members, α-synuclein, was found to be associated with Parkinson's disease and other neurodegenerative disorders, whereas γ-synuclein was linked to several forms of cancer. There are a lot of controversy and exciting debates concerning members of the synuclein family, including their normal functions, toxicity, role in pathology, transmission between cells and intracellular localization. Important findings which remain undisputable for many years are synuclein localization in synapses and their role in the regulation of synaptic vesicle trafficking, whereas their presence and function in mitochondria and nucleus is a debated topic. In this review, we present the data on the localization of synucleins in two intracellular organelles: the nucleus and mitochondria.
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